How about

sub common {
   if ( $_[0] eq $_[1] ) {
         return( $_[0], "", "" );
   } else {
      use bytes;
      my $x = $_[0] ^ $_[1];
      $x =~ m!^(\x00*)!;
      my $pos = length $1;
      my ( $len0, $len1 ) = ( length($_[0])-$pos, length($_[1])-$pos )
+;
      return(
         unpack("a${pos}", $_[0]),
         unpack("x${pos}a*", $_[0]),
         unpack("x${pos}a*", $_[1]),
      );
   }
}
[download]

That way you scan the two strings, but you do it in C instead of doing it in Perl.