It's probably going to be a lot simpler using OS-specific tools and using Runtime.exec()
to run them, but I'll try and give a platform independent answer:
It might be possible to do this platform independently using the Attach API. This comes with the JDK, so to use it just include tools.jar
from your JDK on your program's classpath.
To get a list of virtual machines on the system, use VirtualMachine.list(). You can get/parse arguments from the virtual machine descriptor objects that are returned from this.
The attach API also allows you to load agents into already-running Java processes. Since you want to kill a Java process, you can write a Java agent that simply runs System.exit() (or if you really want it dead use Runtime.halt() instead) when the agent loads.
Once you identify the one you want to kill, attach to it and load the killer agent (the agent has to be built as a JAR file, accessible to the Java process it needs to be loaded into). Shortly after the agent is attached that process should die.
These links might help also:
An Oracle blog on the attach API
Package documentation for java.lang.instrument (has detailed instructions on how to build an agent JAR)