Take a look at the PHP Java extension and/or the PHP Servlet server API. They allow you to instantiate Java classes and reference/invoke members within them. The Servlet extension allows the PHP engine itself to run on the Java Server which should improve Java performance in your PHP code tremendously (not to mention your server's system resources).
Unfortunately, these features are not covered in the PHP manual. However, if you look at the PHP source distribution in ext/java/README and sapi/servlet/README you should get all the information you need.
You'd still have to do all the normal EJB lookup stuff (which you might opt to encapsulate in a Java class instead of trying to do it all from PHP).
If you can't modify the Java Server and install your PHP and Java extensions into it you might have to live with the PHP Java extension and starting up your own local JVM (i.e. instead of the PHP Servlet way).
Alex