read the output from java exec

You already have the process-object (name pr). You can get the Input-, Output- and Errorstream. In your case you want pr.getInputStream(). Read from that, that is connected to the output of the process.

Note that we're reading the process output line by line into our StringBuilder. Due to the try-with-resources statement we don't need to close the stream manually. The ProcessBuilder class let's us submit the program name and the number of arguments to its constructor.

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;

public class ProcessOutputExample
{
    public static void main(String[] arguments) throws IOException,
            InterruptedException
    {
        System.out.println(getProcessOutput());
    }

    public static String getProcessOutput() throws IOException, InterruptedException
    {
        ProcessBuilder processBuilder = new ProcessBuilder("java",
                "-version");

        processBuilder.redirectErrorStream(true);

        Process process = processBuilder.start();
        StringBuilder processOutput = new StringBuilder();

        try (BufferedReader processOutputReader = new BufferedReader(
                new InputStreamReader(process.getInputStream()));)
        {
            String readLine;

            while ((readLine = processOutputReader.readLine()) != null)
            {
                processOutput.append(readLine + System.lineSeparator());
            }

            process.waitFor();
        }

        return processOutput.toString().trim();
    }
}

Prints:

java version "1.8.0_45"
Java(TM) SE Runtime Environment (build 1.8.0_45-b15)
Java HotSpot(TM) 64-Bit Server VM (build 25.45-b02, mixed mode)

Use getErrorStream().

BufferedReader in = new BufferedReader(new InputStreamReader(pr.getErrorStream()));

EDIT:

You can use ProcessBuilder (and also read the documentation)

ProcessBuilder   ps=new ProcessBuilder("java.exe","-version");

//From the DOC:  Initially, this property is false, meaning that the 
//standard output and error output of a subprocess are sent to two 
//separate streams
ps.redirectErrorStream(true);

Process pr = ps.start();  

BufferedReader in = new BufferedReader(new InputStreamReader(pr.getInputStream()));
String line;
while ((line = in.readLine()) != null) {
    System.out.println(line);
}
pr.waitFor();
System.out.println("ok!");

in.close();
System.exit(0);