Frankly, I don't see enough information here to offer substantive advice... so let me raise some more questions:

• Why are you calling the shell script from Perl? Does it return a value or values needed by the Perl script?
• What do you expect to happen after the shell script terminates?
• Have you read the documentation for system and exec? (and consider also the capabilities in IPC::Run as suggested by keszler.

You also need to tell us the answers to colwellj's questions.

Then, perhaps (likely) we can be of more direct assistance.

Update: Oh, yes -- is there some reason why a direct approach -- translating your shell script to Perl (which can do almost anything your shell can) -- is not feasible?