And that situation has made Ferguson even more grateful for Serbia international Vidic.
"Nemanja was magnificent," said the United manager. "It was the best performance you are likely to see from a natural centre-half. His reading of the game is excellent and he is as tough as nails. He was absolutely superb."
Rooney gave United the lead from their first attack, but was replaced after six minutes following a hamstring injury.
"Wayne scored a good goal but he will be out for about three weeks now. Hopefully it is no longer," said Ferguson.
Rooney's injury could provide an opportunity for Carlos Tevez to impress Ferguson as negotiations continue over a new contract, although the Argentina striker picked up a knock during the first half but managed to complete the match.
"Carlos limped through the second half and Jonny limped through virtually the whole game," Ferguson said. "We will have to assess them and see how they are. We need our best team on Saturday because Bolton are a big side."
With a game in hand, United are two points behind Liverpool and could go to the top by beating Bolton on Saturday.
"I don't mind when we go top as I always feel it is the best position to be in," Ferguson said. "Hopefully we will be there by Saturday night, so we need to try and patch the injured players back up."