The following does what you need:

use strict;
use warnings;

chomp(my @version = <DATA>);

print join "\n",
@version = 
    map { join '.', unpack 'C*', $_ }
    sort
    map { pack 'C*', split /\./, $_ } @version;

__DATA__
1.2.3
1.3.4
1.2.31
1.12
1.12.1
1.12.12
[download]

Basically, it converts each number part to a byte value, so the resulting version string is fixed-width (for the number of fields it has) and can be efficiently sorted. Then it sorts and converts back.