He says his decision to name Rooney as a substitute against Fulham was purely down to his fitness levels.
"Rooney wasn't as fit [as the other players]," Sir Alex asserted. "Wayne's said that himself. He needs a few games.
"I wanted to play Robin van Persie at Old Trafford, although I knew he wasn't 100 per cent fit either. It was only because we lost the second goal that I was forced to leave Robin on. I'd have rather taken him off with 20 minutes to go.
"I couldn't have started both of them and I wanted to start van Persie for his first game at Old Trafford. Wayne's a bit behind the other players in terms of fitness. He's not as advanced as Shinji Kagawa or the other midfield players, for example.
"It wasn't an easy choice because I had to leave out a very good player and a player who can score you goals. His goalscoring is getting better all the time. So that's not an easy decision, but it was done."