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The most straightforward way to prevent something from being accessed with a browser is to not put it in a web-accessible directory. Under most default Linux/Unix configurations, that means putting it somewhere which is not under /var/www, /var/html, /var/httpd, or /home/(any user)/public_html.
You can set the file to be owned by the user and/or group that you want to have sole access to it, then only give read and execute permissions to that user/group. If the file can't be read or executed by the user the web server runs as, then the web server can't make it available to remote users.
There are various ways for the Perl code to detect whether it's being run under a CGI interface and/or whether it's being run on the command line, some of which are described in this StackOverflow question and its answers.
If you turn off CGI support in your web server configuration (e.g., for apache, disable mod_cgi to turn it off globally, or set Options -ExecCGI to disable it for individual directories), then it will not be possible to run the Perl code, although it will still be possible for users to view the source file unless other measures are taken as described above.

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