untested, but this should do the trick.

#!/usr/bin/perl
# Script to go through file and count the number 
# of times an ip appears;
use strict;
use warnings;

my $file = 'd:\temp\file.csv';
my %hash;

open (FILE, $file) or die "Can't open $file: $!\n";

while (<FILE>){
  my($src, $dst, $rule1) = split /,/, 3;
  $hash{$src}++;
}

for my $ip (keys %hash){
   print "$ip was seen $hash{$ip} times\n";
}
[download]

Update: For some unknown reason I reposted the original code instead of mine. So here it is