Last season's top scorer for the Reds eventually came off the bench to play his part in the victory, but he suffered a bad gash to his thigh moments from the end and will be sidelined for around four weeks as a result.
Media debate on the striker's future followed his omission, but the speculation was soon rubbished by Wayne himself and then, on Thursday night, by United chief executive David Gill. The manager, meanwhile, says his decision to name Rooney as a substitute 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."
Chief executive Gill was asked about Rooney's future while in Monaco for the Champions League draw.