chomp(my @files = <DATA>);  ## added 

sub by_id {
    # extract numbers
    my ($A) = $a =~ /.+?-(\d+)\..+$/; # changed
    my ($B) = $b =~ /.+?-(\d+)\..+$/; # changed
    # return comparison
    return $A <=> $B;
}

for my $f (sort by_id @files) {
    print $f,$/;
}

__DATA__
abcd1_abc_123456.abc1a_A.201307290800-0900-0.gz
abcd1_abc_123456.abc1a_A.201307290800-0900-1.gz
abcd1_abc_123456.abc1a_A.201307290800-0900-10.gz
abcd1_abc_123456.abc1a_A.201307290800-0900-11.gz
abcd1_abc_123456.abc1a_A.201307290800-0900-2.gz
abcd1_abc_123456.abc1a_A.201307290800-0900-3.gz