The web server has no idea that the CGI program is in Perl - CGI is just an interface specification and can be used to execute programs written in Perl, C, bash, or any other language.
When the server executes a CGI program, it basically1 just does the same thing as if you had typed filename.cgi on the command line. In the case of Perl programs on unix-like environments, the first line of the file will be something like #!/usr/bin/perl which tells the operating system to run the code through the Perl interpreter without the caller (i.e., the web server) needing to know that it's dealing with a Perl program.
1 The web server also sets up various things in the environment, so that the CGI program is able to get information about the HTTP request that invoked it, but that's beside the point.
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