You could achieve this with the Perl debugger. The trick is to get an interactive debugger session into your CGI script as you interact with it through a web page. I do this with Catalyst apps and it fires of a terminal on my system when the code encounters a "$DB::single=1;" line. I'm not sure exactly how to acheive this with a simple CGI script but this thread here Debugging CGI/PERL has some advice on that.
Once you have the debugger session you can monitor a variable by setting a watch expression (w NAME_OF_VARIABLE), which will be triggered whenever the value of the variable changes.