mod_perl had the issue that it had hooks deep into the webserver, which wasn't "shared hosting safe" mod_php had less hooks and some basic cross-vhost-access mitigations (Safe_mode oben_basedir etc.) which allowed independent users to put PHP scripts on the same server, which in turn made web hosting cheap.
When I last used PHP (about 5 years ago) it was common to use it via FastCGI "for performance". I'm not sure how true that reasoning was, or how the speedups of 7.x have changed things, but (Fast/S/whatever)CGI still seems prevalent.
PHP was using CGI like Perl. And then PHP had Apache's mod_php, which I believe is still widely used today.
Perl, of course, had mod_perl. And later, PSGI/Plack followed by Catalyst, Mojolicious, Dancer, etc.