mod_perl isn't available on many servers, and without that, PHP outperforms Perl. It's also easier to embed a few lines of PHP inside your page than it is to wrap your page around the equivalent in Perl code, leaving Perl the winner only in situations where (a) you have root on the server or (b) you're doing some algorithms-heavy programming where Perl's power and coding efficiency makes it the better choice.

Basically, PHP is designed to be easy. Perl is designed for coding efficiency. Most people are going to prefer the former if they have to choose between the two.

Learning both is best.