#!perl
use strict;
use warnings;

# ...

open $IN1, "<", $infile1 or die "cannot open $infile1: $!\n";
open $IN2, "<", $infile2 or die "cannot open $infile2: $!\n";
open $OUT, ">", $outfile or die "cannot open $outfile: $!\n";

my %pair = ();

while (<$IN1>) {
  chomp;
  s/^(\w+)\s+(\w+)$/$1 $2/; # just one space between keys
  $pair{$_} = 1;
}

while (<$IN2>) {
  chomp;
  s/^(\w+)\s+(\w+)$/$2 $1/; # swap keys
  if (exists $pair{$_}) {
    print $OUT "$_\n";
    delete $pair{$_};
  }
}

close $IN1;
close $IN2;
close $OUT;