You could use the system function to run perl on some args supplied as CGI input, but this can be very dangerous since a user could enter commands which when fed to perl erase things in your web directory, for example (or worse.) It is really quite easy for this to happen. You should certainly use Taint mode and check all input very carefully. In fact, I've never done anything like that just because I'm afraid I might overlook some security pitfall. It is safer if you have a fixed set of commands that can be fed to perl and just allow those (perhaps checking if user input matches one of the allowed ones.) I'm not sure this is what you meant, but it sounded like that. (If you exhibit your script here, I'm sure you will get valuable advice about possible problems.)
Check out Ovid's cgi course for examples of pitfalls and a lot more.
chas