Early goals from the former Everton man and striker Robin van Persie had the hosts two goals up with just 22 minutes played but Diafra Sakho headed in from a corner just before the break to edge one back.
The game got worse Louis van Gaal’s side as Rooney lashed out at Stewart Downing with a high foot and the attacker received a straight red from referee Lee Mason.
"It was a break-out of a set-play of ours and he makes a professional foul, I think you can call it like that," he told the BBC. "I don't think Wayne wanted to do it that way but he did it and you can give a red card."
Van Gaal was facing big problems before the game, with Marcos Rojo the only fit senior centre-back for selection, forcing Van Gaal to bring in youngsters Paddy McNair and Tom Thorpe into the squad.
He explained: "Luke Shaw was always injured. He had a little cramp and it was amazing he lasted. Also, Paddy McNair played a very good match and I'm very pleased for him that we won.
"The rhythm of the game is very high. You cannot compare it with Germany and Spain. There is always pressure on the ball and most play physically. We have to keep the ball and then we can improve our play.
"We had to fight and fight and fight again. I'm very pleased with my players' attitude. We played very well in the first half – good attacking and effective football. Very dominant."