Sort::Key::Natural seems the best way here, so I'd stick with moritz's suggestion.

But if you want to experiment with sort, it can be done with a custom sort subroutine. An example (tested):

#!/usr/bin/perl -w
use strict;

sub by_the_number_at_the_end {
    $a =~ /(\d+)$/;
    my $end_of_a = $1;
    $b =~ /(\d+)$/;
    my $end_of_b = $1;
    return -1 if $end_of_a < $end_of_b;
    return 0  if $end_of_a == $end_of_b;
    return 1  if $end_of_a > $end_of_b;
}

my @array=("ch1","ch11","ch2","ch5","ch55","ch16");

print join ("\n", sort by_the_number_at_the_end @array);
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Regards,
Luke