Just extend your existing regular expression a bit will do the trick -

use strict;

while (<DATA>) {
    s/(\d+|\.)/ $1 eq '.' ? '' : sprintf "%03d", $1 /eg;
    print;
}

__DATA__
127.0.0.1
256.123.12.1
256.12.31.21
[download]

And the output -

127000000001
256123012001
256012031021
[download]