After searching CPAN, it looks like the only contender is the JavaScript module - "Perl extension for executing embedded JavaScript" (but you already mentioned it). I cannot recommend it personally since I've never seen the need to use JavaScript in Perl. But you just want to extract links that are created with JavaScript. So I think that it should fit the bill.

Of course, I would just write Perl code to mimic the functionality of the JavaScript.

Update: removed references to JavaScript::Toolbox since it's not relevant.