Yeah, you can pass parameters to system or exec. There are some fine points about parameters on windows and dos(which I don't use), but try your stuff and report what errors you get.

#!/usr/bin/perl
use strict;
use warnings;

my $param1 = 'whatever';
my $param2 = 'whoever'; 

my $programtorun  =  'program_name';
my @parameters    =  ( $param1, $param2  );   
my @cmdline       =  ( $programtorun, @parameters );
system (@cmdline);  # will run cmd, and then return to script 
#exec (@cmdline);   # will replace currently running script
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