But this script.pl file also gets changed... the directory path is /main/script.pl -- Script file. /main/test/*.pl files -- perl files.

Let's suppose you write your script file like this (I prefer using curly braces around regexes when the slash is part of the pattern or replacement):

#!/usr/bin/perl

use strict;
use warnings;

# check for valid usage (user must provide a directory path):

(@ARGV == 1 and -d $ARGV[0]) or die "Usage: $0 /path/to/scripts\n";

my $path = shift;
{
    local $/;   # set input record separator to undef (slurp-mode read
+ing)

    for my $file (<$path/*.pl>)  # use a file glob 
    {
        open( F, "<", $file ) or next;
        $_ = <F>;
        close F;
        s{/usr/bin/perl}{/test/test/test}g;
        s{/ggg/ggg/www}{/zzz/zzz/zzz}g;
        s{/jjj/jjj/jjj}{/aaa/aaa/aaa}g;
        open( F, ">", $file ) or die "$file: $!";
        print F;
        close F;
    }
}
[download]

When you put that script file in a directory other than the one that you provide as a command-line arg when you run it (or if you put it in the same directory, but give it a name that does not end in ".pl"), the script will not edit/rewrite itself.