I solved the problem (How to connect multiple database using spring and Hibernate) in this way, I hope it will help :)
NOTE: I have added the relevant code, kindly make the dao with the help of impl I used in the below mentioned code.
web.xml
<?xml version="1.0" encoding="UTF-8"?>
<web-app xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xmlns="http://java.sun.com/xml/ns/javaee" xmlns:web="http://java.sun.com/xml/ns/javaee/web-app_2_5.xsd"
    xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/web-app_3_0.xsd"
    id="WebApp_ID" version="3.0">
    <display-name>MultipleDatabaseConnectivityInSpring</display-name>
    <welcome-file-list>
        <welcome-file>index.jsp</welcome-file>
    </welcome-file-list>
     <servlet>
        <servlet-name>dispatcher</servlet-name>
        <servlet-class>org.springframework.web.servlet.DispatcherServlet</servlet-class>
         <load-on-startup>1</load-on-startup>
    </servlet>
     <listener>
        <listener-class>org.springframework.web.context.ContextLoaderListener</listener-class>
    </listener> 
    <context-param>
        <param-name>contextConfigLocation</param-name>
        <param-value>
            /WEB-INF/dispatcher-servlet.xml
        </param-value>
    </context-param>
    <servlet-mapping>
        <servlet-name>dispatcher</servlet-name>
        <url-pattern>*.htm</url-pattern>
    </servlet-mapping>
    <session-config>
        <session-timeout>30</session-timeout>
    </session-config>
</web-app>
persistence.xml
<?xml version="1.0" encoding="UTF-8"?>
<persistence version="1.0"
    xmlns="http://java.sun.com/xml/ns/persistence" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:schemaLocation="http://java.sun.com/xml/ns/persistence http://java.sun.com/xml/ns/persistence/persistence_1_0.xsd">
    <persistence-unit name="localPersistenceUnitOne"
        transaction-type="RESOURCE_LOCAL">
        <provider>org.hibernate.ejb.HibernatePersistence</provider>
        <class>in.india.entities.CustomerDetails</class>
        <exclude-unlisted-classes />
        <properties>
            <property name="hibernate.dialect" value="org.hibernate.dialect.PostgreSQLDialect" />
            <property name="hibernate.connection.driver_class" value="org.postgresql.Driver" />
            <property name="hibernate.jdbc.batch_size" value="0" />
            <property name="hibernate.show_sql" value="false" />
            <property name="hibernate.connection.url" value="jdbc:postgresql://localhost:5432/shankar?sslmode=require" />
            <property name="hibernate.connection.username" value="username" />
            <property name="hibernate.connection.password" value="password" />
            <property name="hibernate.hbm2ddl.auto" value="update" />
        </properties>
    </persistence-unit>
    <persistence-unit name="localPersistenceUnitTwo"
        transaction-type="RESOURCE_LOCAL">
        <provider>org.hibernate.ejb.HibernatePersistence</provider>
        <class>in.india.entities.CompanyDetails</class>
        <exclude-unlisted-classes />
        <properties>
            <property name="hibernate.dialect" value="org.hibernate.dialect.PostgreSQLDialect" />
            <property name="hibernate.connection.driver_class" value="org.postgresql.Driver" />
            <property name="hibernate.jdbc.batch_size" value="0" />
            <property name="hibernate.show_sql" value="false" />
            <property name="hibernate.connection.url" value="jdbc:postgresql://localhost:5432/shankarTwo?sslmode=require" />
            <property name="hibernate.connection.username" value="username" />
            <property name="hibernate.connection.password" value="password" />
            <property name="hibernate.hbm2ddl.auto" value="update" />
        </properties>
    </persistence-unit>
</persistence>
dispatcher-servlet
<?xml version="1.0" encoding="UTF-8"?>
<beans xmlns="http://www.springframework.org/schema/beans"
    xmlns:task="http://www.springframework.org/schema/task" xmlns:p="http://www.springframework.org/schema/p"
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:context="http://www.springframework.org/schema/context"
    xmlns:mvc="http://www.springframework.org/schema/mvc" xmlns:tx="http://www.springframework.org/schema/tx"
    xmlns:aop="http://www.springframework.org/schema/aop" xmlns:util="http://www.springframework.org/schema/util"
    default-autowire="byName"
    xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans.xsd 
      http://www.springframework.org/schema/context http://www.springframework.org/schema/context/spring-context-3.0.xsd  
      http://www.springframework.org/schema/aop  http://www.springframework.org/schema/aop/spring-aop-3.0.xsd 
      http://www.springframework.org/schema/task http://www.springframework.org/schema/task/spring-task-3.0.xsd
      http://www.springframework.org/schema/tx http://www.springframework.org/schema/tx/spring-tx-3.0.xsd http://www.springframework.org/schema/mvc 
      http://www.springframework.org/schema/mvc/spring-mvc-3.0.xsd">
    <!-- Configure messageSource -->
    <mvc:annotation-driven />
    <context:component-scan base-package="in.india.*" />
    <bean id="messageResource"
        class="org.springframework.context.support.ResourceBundleMessageSource"
        autowire="byName">
        <property name="basename" value="messageResource"></property>
    </bean>
    <bean
        class="org.springframework.web.servlet.view.InternalResourceViewResolver">
        <property name="prefix">
            <value>/WEB-INF/jsp/</value>
        </property>
        <property name="suffix">
            <value>.jsp</value>
        </property>
    </bean>
    <bean id="entityManagerFactoryOne"
        class="org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean"
        autowire="constructor">
        <property name="persistenceUnitName" value="localPersistenceUnitOne" />
    </bean>
    <bean id="messageSource"
        class="org.springframework.context.support.ResourceBundleMessageSource"
        autowire="byName">
        <property name="basename" value="messageResource" />
    </bean>
    <bean id="entityManagerFactoryTwo"
        class="org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean"
        autowire="constructor">
        <property name="persistenceUnitName" value="localPersistenceUnitTwo" />
    </bean>
    <bean id="manager1" class="org.springframework.orm.jpa.JpaTransactionManager">
        <property name="entityManagerFactory" ref="entityManagerFactoryOne" />
    </bean>
    <bean id="manager2" class="org.springframework.orm.jpa.JpaTransactionManager">
        <property name="entityManagerFactory" ref="entityManagerFactoryTwo" />
    </bean>
    <tx:annotation-driven transaction-manager="manager1" />
    <tx:annotation-driven transaction-manager="manager2" />
    <!-- declare dependies here -->
    <bean class="in.india.service.dao.impl.CustomerServiceImpl" />
    <bean class="in.india.service.dao.impl.CompanyServiceImpl" />
    <!-- Configure MVC annotations -->
    <bean
        class="org.springframework.web.servlet.mvc.annotation.DefaultAnnotationHandlerMapping" />
    <bean
        class="org.springframework.web.servlet.mvc.annotation.AnnotationMethodHandlerAdapter" />
    <bean
        class="org.springframework.http.converter.json.MappingJacksonHttpMessageConverter" />
</beans>
java class to persist into one database
package in.india.service.dao.impl;
import in.india.entities.CompanyDetails;
import in.india.service.CompanyService;
import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import org.springframework.transaction.annotation.Transactional;
public class CompanyServiceImpl implements CompanyService {
    @PersistenceContext(unitName = "entityManagerFactoryTwo")
    EntityManager entityManager;
    @Transactional("manager2")
    @Override
    public boolean companyService(CompanyDetails companyDetails) {
        boolean flag = false;
        try 
        {
            entityManager.persist(companyDetails);
            flag = true;
        } 
        catch (Exception e)
        {
            flag = false;
        }
        return flag;
    }
}
java class to persist in another database 
package in.india.service.dao.impl;
import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import org.springframework.transaction.annotation.Transactional;
import in.india.entities.CustomerDetails;
import in.india.service.CustomerService;
public class CustomerServiceImpl implements CustomerService {
    @PersistenceContext(unitName = "localPersistenceUnitOne")
    EntityManager entityManager;
    @Override
    @Transactional(value = "manager1")
    public boolean customerService(CustomerDetails companyData) {
        boolean flag = false;
        entityManager.persist(companyData);
        return flag;
    }
}
customer.jsp
<%@page language="java" contentType="text/html; charset=ISO-8859-1"
    pageEncoding="ISO-8859-1"%>
<%@taglib uri="http://www.springframework.org/tags/form" prefix="form"%>
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
<title>Insert title here</title>
</head>
<body>
    <center>
        <h1>SpringWithMultipleDatabase's</h1>
    </center>
    <form:form method="GET" action="addCustomer.htm"  modelAttribute="customerBean" >
        <table>
            <tr>
                <td><form:label path="firstName">First Name</form:label></td>
                <td><form:input path="firstName" /></td>
            </tr>
            <tr>
                <td><form:label path="lastName">Last Name</form:label></td>
                <td><form:input path="lastName" /></td>
            </tr>
            <tr>
                <td><form:label path="emailId">Email Id</form:label></td>
                <td><form:input path="emailId" /></td>
            </tr>
            <tr>
                <td><form:label path="profession">Profession</form:label></td>
                <td><form:input path="profession" /></td>
            </tr>
            <tr>
                <td><form:label path="address">Address</form:label></td>
                <td><form:input path="address" /></td>
            </tr>
            <tr>
                <td><form:label path="age">Age</form:label></td>
                <td><form:input path="age" /></td>
            </tr>
            <tr>
                <td><input type="submit" value="Submit"/></td>
             </tr>
        </table>
    </form:form>
</body>
</html>
company.jsp
<%@ page language="java" contentType="text/html; charset=ISO-8859-1" pageEncoding="ISO-8859-1"%>
<%@taglib uri="http://www.springframework.org/tags/form" prefix="form"%>
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
<title>ScheduleJobs</title>
</head>
<body>
 <center><h1>SpringWithMultipleDatabase's</h1></center>
 <form:form method="GET" action="addCompany.htm"  modelAttribute="companyBean" >
 <table>
    <tr>
        <td><form:label path="companyName">Company Name</form:label></td>
        <td><form:input path="companyName" /></td>
    </tr>
    <tr>
        <td><form:label path="companyStrength">Company Strength</form:label></td>
        <td><form:input path="companyStrength" /></td>
    </tr>
    <tr>
        <td><form:label path="companyLocation">Company Location</form:label></td>
        <td><form:input path="companyLocation" /></td>
    </tr>
     <tr>
        <td>
            <input type="submit" value="Submit"/>
        </td>
    </tr>
 </table>
 </form:form>
</body>
</html>
index.jsp
<%@ page language="java" contentType="text/html; charset=ISO-8859-1"
    pageEncoding="ISO-8859-1"%>
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
<title>Home</title>
</head>
<body>
 <center><h1>Multiple Database Connectivity In Spring sdfsdsd</h1></center>
<a href='customerRequest.htm'>Click here to go on Customer page</a>
<br>
<a href='companyRequest.htm'>Click here to go on Company page</a>
</body>
</html>
success.jsp
<%@ page language="java" contentType="text/html; charset=ISO-8859-1"
    pageEncoding="ISO-8859-1"%>
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
<title>ScheduleJobs</title>
</head>
<body>
 <center><h1>SpringWithMultipleDatabase</h1></center>
    <b>Successfully Saved</b>
</body>
</html>
CompanyController
package in.india.controller;
import in.india.bean.CompanyBean;
import in.india.entities.CompanyDetails;
import in.india.service.CompanyService;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Controller;
import org.springframework.ui.Model;
import org.springframework.ui.ModelMap;
import org.springframework.web.bind.annotation.ModelAttribute;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.servlet.ModelAndView;
@Controller
public class CompanyController {
    @Autowired
    CompanyService companyService;
    @RequestMapping(value = "/companyRequest.htm", method = RequestMethod.GET)
    public ModelAndView addStudent(ModelMap model) {
        CompanyBean companyBean = new CompanyBean();
        model.addAttribute(companyBean);
        return new ModelAndView("company");
    }
    @RequestMapping(value = "/addCompany.htm", method = RequestMethod.GET)
    public ModelAndView companyController(@ModelAttribute("companyBean") CompanyBean companyBean, Model model) {
        CompanyDetails  companyDetails = new CompanyDetails();
        companyDetails.setCompanyLocation(companyBean.getCompanyLocation());
        companyDetails.setCompanyName(companyBean.getCompanyName());
        companyDetails.setCompanyStrength(companyBean.getCompanyStrength());
        companyService.companyService(companyDetails);
        return new ModelAndView("success");
    }
}
CustomerController
package in.india.controller;
import in.india.bean.CustomerBean;
import in.india.entities.CustomerDetails;
import in.india.service.CustomerService;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Controller;
import org.springframework.ui.Model;
import org.springframework.ui.ModelMap;
import org.springframework.web.bind.annotation.ModelAttribute;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.servlet.ModelAndView;
@Controller
public class CustomerController {
    @Autowired
    CustomerService customerService;
    @RequestMapping(value = "/customerRequest.htm", method = RequestMethod.GET)
    public ModelAndView addStudent(ModelMap model) {
        CustomerBean customerBean = new CustomerBean();
        model.addAttribute(customerBean);
        return new ModelAndView("customer");
    }
    @RequestMapping(value = "/addCustomer.htm", method = RequestMethod.GET)
    public ModelAndView customerController(@ModelAttribute("customerBean") CustomerBean customer, Model model) {
        CustomerDetails customerDetails = new CustomerDetails();
        customerDetails.setAddress(customer.getAddress());
        customerDetails.setAge(customer.getAge());
        customerDetails.setEmailId(customer.getEmailId());
        customerDetails.setFirstName(customer.getFirstName());
        customerDetails.setLastName(customer.getLastName());
        customerDetails.setProfession(customer.getProfession());
        customerService.customerService(customerDetails);
        return new ModelAndView("success");
    }
}
CompanyDetails Entity
package in.india.entities;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.GeneratedValue;
import javax.persistence.GenerationType;
import javax.persistence.Id;
import javax.persistence.SequenceGenerator;
import javax.persistence.Table;
@Entity
@Table(name = "company_details")
public class CompanyDetails {
    @Id
    @SequenceGenerator(name = "company_details_seq", sequenceName = "company_details_seq", initialValue = 1, allocationSize = 1)
    @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = "company_details_seq")
    @Column(name = "company_details_id")
    private Long companyDetailsId;
    @Column(name = "company_name")
    private String companyName;
    @Column(name = "company_strength")
    private Long companyStrength;
    @Column(name = "company_location")
    private String companyLocation;
    public Long getCompanyDetailsId() {
        return companyDetailsId;
    }
    public void setCompanyDetailsId(Long companyDetailsId) {
        this.companyDetailsId = companyDetailsId;
    }
    public String getCompanyName() {
        return companyName;
    }
    public void setCompanyName(String companyName) {
        this.companyName = companyName;
    }
    public Long getCompanyStrength() {
        return companyStrength;
    }
    public void setCompanyStrength(Long companyStrength) {
        this.companyStrength = companyStrength;
    }
    public String getCompanyLocation() {
        return companyLocation;
    }
    public void setCompanyLocation(String companyLocation) {
        this.companyLocation = companyLocation;
    }
}
CustomerDetails Entity
package in.india.entities;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.GeneratedValue;
import javax.persistence.GenerationType;
import javax.persistence.Id;
import javax.persistence.SequenceGenerator;
import javax.persistence.Table;
@Entity
@Table(name = "customer_details")
public class CustomerDetails {
    @Id
    @SequenceGenerator(name = "customer_details_seq", sequenceName = "customer_details_seq", initialValue = 1, allocationSize = 1)
    @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = "customer_details_seq")
    @Column(name = "customer_details_id")
    private Long customerDetailsId;
    @Column(name = "first_name ")
    private String firstName;
    @Column(name = "last_name ")
    private String lastName;
    @Column(name = "email_id")
    private String emailId;
    @Column(name = "profession")
    private String profession;
    @Column(name = "address")
    private String address;
    @Column(name = "age")
    private int age;
    public Long getCustomerDetailsId() {
        return customerDetailsId;
    }
    public void setCustomerDetailsId(Long customerDetailsId) {
        this.customerDetailsId = customerDetailsId;
    }
    public String getFirstName() {
        return firstName;
    }
    public void setFirstName(String firstName) {
        this.firstName = firstName;
    }
    public String getLastName() {
        return lastName;
    }
    public void setLastName(String lastName) {
        this.lastName = lastName;
    }
    public String getEmailId() {
        return emailId;
    }
    public void setEmailId(String emailId) {
        this.emailId = emailId;
    }
    public String getProfession() {
        return profession;
    }
    public void setProfession(String profession) {
        this.profession = profession;
    }
    public String getAddress() {
        return address;
    }
    public void setAddress(String address) {
        this.address = address;
    }
    public int getAge() {
        return age;
    }
    public void setAge(int age) {
        this.age = age;
    }
}