...

open my $fh2, '<', 'domains.txt' or die "could not open domains.txt: $!\n";
my %domains = map { chomp; $_ => 1 } <$fh2>;
close $fh2;

open my $fh, "<", "output.txt" or die "could not open output.txt: $!\n";

my %data;
while (<$fh>) {
	chomp;
	$_ =~ m/(.*?)\s++(\d++)/;
	next unless $domains{$1};

...