Ruud's first goal came form the penalty spot sending the goalkeeper the wrong way.
Van Nistelrooy is now tied with Wayne Rooney as the championship's leading scorer.
"Wayne's so young and doing so well on a big stage," Ruud said after the match. "That's a fantastic achievement, though so are the whole English team. We're happy to say we're in the quarter-finals as well. To go through this group the way we have was very strange, but we're there now."