Rooney (ankle), Nemanja Vidic (leg) and Edwin van der Sar (virus) were all missing for the triumph.
"Wayne came out for training on Friday and we thought he would make today," said Ferguson.
"But he just felt it again. At that point, we said no. There was no point.
"Vidic got a knock in training. He will be okay for Tottenham next Sunday. Edwin will maybe be another week or so."