I would do it like this:

#!/usr/bin/perl
use strict;
use warnings;

my(@hosts, @ports);

while (<DATA>) {
  push @hosts, $1 while /HOST=(\S*?)\./g; # nongreedy quantifier *?
  push @ports, $1 while /PORT=(\S*)/g;
}

print "Hosts: ", join(", ", sort @hosts), "\n";
print "Ports: ", join(", ", sort @ports), "\n";

__DATA__
HOST=machine1-basement.xyz.com PORT=1234 HOST=machine2-attic.xyz.com P
+ORT=9999 HOST=machine3-garage.xyz.com PORT=5555
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