Do not accept input from end users that will be directly interpreted as source code. If this is a business requirement, validate all the input on the application and remove all the data that could be directly interpreted as Perl source code.
This vulnerability is not difficult to leverage. Perl is a high level language for which there are vast resources available. Successful exploitation requires knowledge of the programming language, access to the source code or the ability to produce source code for use in such attacks, and minimal attack skills.