use strict;
use warnings;

use 5.010;

my $rxSep = qr{[-_.]};

my @versions = qw{
   1.2.3.4
   2.6
   3_4_9
   4-2-13-5
   5
};

foreach my $version ( @versions )
{
    ( my $newVersion = $version ) =~
       s{((?:\d+$rxSep)+)*(\d+)(?!$rxSep)}
       { my $ver = $2; ( defined $1 ? $1 : q{} ) . ++ $ver }e;
    say qq{$version => $newVersion};
}