The 27-year-old has been deployed as a midfielder in recent weeks instead of in his trademark position as an attacker, which Sir Alex believes is the reason for his subdued display in United's 2-2 draw at West Ham.
The Scot told reporters: “As far as taking him off on Wednesday [is concerned], it’s simply because he wasn’t playing as well as Shinji [Kagawa] was.
“We had to get that goal that mattered and of course there are so many games [in which] Wayne Rooney is better than most players. But on the night Shinji was playing so well.
“His selection of passes is good. He has great composure on the ball and his decision-making is good.”
Sir Alex explained: “I’d already given the fourth official the card.
“Javier [Hernandez] was stood on the touchline when we scored the second goal.
“I think if I’d have changed my decision then I think we’d have won the game because Shinji was doing really well.”