Frankly, few developers are writing performant enough code for this to matter. A good PHP programmer will write faster apps than an average Java programmer, and vice versa. And if you're not a good programmer, it won't matter, you'll make them both slow.
Don't get me wrong, you should certainly use an opcode cache for PHP. But if you are, the difference in performance between Java and PHP is unlikely to be the determining factor in your app's performance.
Java has threading and persistence, so if those are important use Java. PHP is super easy to deploy, and does not require extensive tuning of things like heap & garbage collection, so if that's important to you, use PHP.
Unless you're a decent sized website, use the one you know best. You'll have written it twice and optimized it before you write it once in the other language.