He was left out of the 3-3 draw at Everton on 11 September following allegations about his private life, with Ferguson not wanting to subject Rooney to an expected hostile crowd at his former club.
Ferguson later claimed Rooney was feeling the pressure of the media scrutiny he was under before substituting him at Bolton and leaving him out of the Champions League group win at Valencia and goalless draw at Sunderland.
Ahead of the Black Cats game, Ferguson said: "I have to take the view that this injury has been niggling away for a while and he kept on playing.
"I have to be dead sure that I am doing the right thing because Wayne has not been doing himself justice. I think in a week he will be fine."
Rooney came into this season on the back of a poor World Cup in South Africa with the cause believed to be a lack of fitness because of an ankle injury suffered in a Champions League match against Bayern Munich in March.
But Rooney said: "Towards the end of last season I was injured but during the World Cup, I trained every session and had no problems fitness-wise.
I'll keep doing my training and I'm sure the goals will come
"I think in this league you need to keep playing because, if you are not at full fitness, then it's difficult to break teams down."
He added: "When you are going through the run I am now, you just have to keep working hard.
"I know I've been through this before and once one goal goes in, I am sure I will get more but it's just getting that goal.
"If you don't score, and you have chances, you are disappointed. I want to score but I have got a lot of games left in the season. I am sure this run without scoring will end soon.
"I don't do anything different. I train as hard as I can every time I train and I do extra training every day and I've done that since I was a young boy.
"I'll keep doing my training and I'm sure the goals will come.
"I've missed a few games this season. I've played six or seven games this season including England.
"You just want to keep playing consistently now and keep working hard and I'm sure the goals will come."
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.