I attempted to rewrite your code to possibly be what you want.  Could you try to specify exactly what you're trying to do?
import java.util.Scanner;
public class Main
{
    public static void main(String[] args)
    {
       Scanner input = new Scanner(System.in);
       int numberOfStudents = input.nextInt();
       //input.nextLine();
       String[][] partners = new String[2][numberOfStudents];
       for(int i=0; i<numberOfStudents; i++)
       {
          partners[1][i] = input.nextLine();
       }
    }
}
I think you're looking for split.
For example:
    String val="I am a String";
    String [] tabDelimitedVals=val.split(" ");
This is seen in the stack overflow post here:
How to split a string in Java
To read from a file, you can use
BufferedReader br = new BufferedReader(new FileReader("file.txt"));
try {
    StringBuilder sb = new StringBuilder();
    String line = br.readLine();
    while (line != null) {
        sb.append(line);
        sb.append(System.lineSeparator());
        line = br.readLine();
    }
    String everything = sb.toString();
} finally {
    br.close();
} 
The above was taken from: Reading a plain text file in Java
Together, you can do:
BufferedReader br = new BufferedReader(new FileReader("file.txt"));
try {
    String val=br.readLine();
    String [] splitted=val.split(" ");
}
finally {
   br.close();
}