The Scot insisted that the 37-year-old was rested in a bid to keep him fresh ahead of the Red Devils run in and has praised the impact the midfielder has had since returning
The Premier League leaders are unbeaten in the 12 games the 37-year-old has played in since coming out of retirement in January.
But, according to the Scot, the Salford-born star was left out of the United squad at DW Stadium in a bid to keep him fit ahead of crucial run-in which begins at home to Aston Villa on Sunday.
Sir Alex told reporters: "We did the right thing resting him on Wednesday after he played on Sunday.
"It may not have looked that way to the fans, but it was the right thing to do, so he'll be fresh. He'll play on Sunday.
"We could have used him on Wednesday, but you have to remember that three games in seven days would have been a big ask for him."
Scholes' shock comeback at the start of 2012 was seen by many as a gamble by Sir Alex, but it seems to have paid off for the United boss who believes the midfielder has made a big difference to the Red Devils.
"He's shown his influence since he came back, there's no question of that," the 70-year-old said.
"In games at Old Trafford – or in any game actually – he controls the tempo and rhythm. He's just a great player.
"We thought that, with the experience of Ryan [Giggs] in the middle of the pitch, we'd be all right. But, as it transpired, we didn’t show."