It depends on who is calling who or if both are running in parallel. If JSP is calling perl,

Runtime.getRuntime().exec(...)
[download]

can run any shell command, including invocation of a Perl program and give it arguments in the command line which Perl picks up as @ARGV.

If it's the other way round, there are many ways for Perl to invoke the .jsp, including using ``, system(), but the most comprehensive is IPC::Run3.

If it's parallel, then maybe communicate through a named pipe.