However, Ipswich manager George Burley didn't hold back in his after match comments when he accused the Dutch forward of diving.
"I went to head the ball and the defender pulled me down so I couldn't head it," said Nistelrooy on the decision.
"It was a clear decision to me and then I just focused on the penalty kick."
Ruud is not letting the furore distract him from his game, and is looking forward to the crucial Champions League clash in Germany.
"It will be a very difficult game, but one win and we are in the final. And with our quality it is possible to do it," he said.
"Leverkusen lost on Saturday while we were winning, but Tuesday is a game on it's own. We know what we have to do and that is the most important thing."