That isn't a Perl problem. Your web server isn't configured to do what you want it to do. It hasn't been told to treat the file as a CGI script.
If you want to treat all .cgi files in a directory and subdirectories as CGI scripts:
<Directory /some/dir/htdocs/>
Options +ExecCGI
AddHandler cgi-script .cgi
</Directory>
If you want to treat all files in a directory and subdirectories as CGI scripts:
<Directory /some/dir/cgi-bin/>
Options +ExecCGI
SetHandler cgi-script
</Directory>
There's also ScriptAlias.
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