The pair were selected to start in the Red Devils' 2-1 League Cup victory over Newcastle on Wednesday evening after prolonged absences from the starting lineup
The England forward was making his first appearance since sustaining a serious leg gash during a Premier League win over Fulham in August.
Meanwhile, Fletcher captained the Red Devils in his first start since November, after taking a prolonged break to treat a bowel condition.
Sir Alex told Sky Sports: "Fletcher and Rooney were both excellent. Wayne tired a bit towards the end but that was to be expected and they have done really well. I'm very pleased first of all to win an all-Premier League division tie and then because Newcastle had a stronger team than us physically but we played some fantastic football and I think we deserved the victory."
"We want to progress as far as we can in the competition and we'll do our best to do that. Winning is always important at this club."
The Scot also had kind words for a young United back four which included the likes of England Under-19 international Michael Keane.
"The young defenders did their best. It was obviously difficult as [Shola] Ameobi is a big lad, a handful. Then they brought [Papiss] Cisse on, who is one of the best players at the club and has a lot of experience. It was a compliment to us that they did that and I think we handled it quite well."
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