my $re = do {
   local *FILE;
   open(FILE, '<', $regexp_file_name)
   or die('...');
   
   local $/;
   qr/@{[<FILE>]}/   # Compile only once.
};

while (<DATA>) {   
   if (@captures = $_ =~ $re) {
      print(join(', ', @captures), $/);
   }
}

__DATA__
abd 123 sdafas 231
gdabd 7364 112 sdafas 785


regexp file (Matches lines with two words of exactly 3 digits.)
===========
\b(\d{3})\b.*?\b(\d{3})\b


output
======
123, 231
112, 785