It is possible to use multiple databases in spring boot.
But spring boot can automatically configure only one database.
You need to configure the second database yourself.
@Bean
@ConfigurationProperties(prefix="second.datasource")
public DataSource secondDataSource(){
  return DataSourceBuilder
        .create()
        .driverClassName("org.h2.Driver")
        .build();
}
If you just need a jdbc connection, this would be already sufficient. As you want to use JPA you need also a second JPA configuration, that uses the second data source.
@Bean(name="secondEntityManager")
public LocalContainerEntityManagerFactoryBean mySqlEntityManagerFactory(EntityManagerFactoryBuilder builder,DataSource secondDataSource){
    return builder.dataSource(secondDataSource)                
        .packages("com.second.entity")
        .build();
}   
You can find the code above and more in this post