The 1-0 defeat, where 37-year-old Scholes was rested, allowed second-placed Manchester City to cut the gap to five points with five games left.
"We did the right thing resting Paul Scholes - he'll play on Sunday. He's shown his influence since he came back," Ferguson told a news conference on Friday.
Scholes retired at the end of last season but was tempted back by Ferguson in January because of a lack of fit players in midfield, although the former England man has continued to be a first choice even with the injury list easing.
His precision passing and occasional eye for goal led Ferguson to label Scholes as one of the best midfielders in the last 20 years, which goes some way to explaining why United struggled to replace him in the close-season.
Bids for Inter Milan's Dutch playmaker Wesley Sneijder were denied by United but their recall of Scholes and general lack of flair has prompted pundits to say this could be one of the worst United sides to win the Premier League title.
They are not quite there yet after Wednesday's wobble but Ferguson believes the championship experience of Scholes and Co means an immediate recovery is likely at Old Trafford on Sunday.
"We were disappointed to lose but we have to put it into perspective. In the treble year  we went through the whole season from December without losing. A couple of years back we lost 4-1 at home to Liverpool and won the league by nine points," he said.
"From the position of a few months ago to where we are today, we have to be delighted. Sunday is very important and we must get back on track. A great thing about our club is we do recover and we have to do that again."
Manchester City boss Roberto Mancini said on Wednesday the title race was over despite his side's 4-0 win over West Bromwich Albion but most commentators think he was playing mind games to try to destabilise United.
Ferguson said: "I think he has maybe picked the wrong time to say it - there are still five games to go. The Premier League is fascinating. Our experience will help us and Sunday's game is the one to focus on."
Villa are not totally safe from relegation and manager Alex McLeish, who played for Ferguson at Aberdeen, is under pressure from fans after struggling to mould a youthful winning side since his shock move from bitter city rivals Birmingham City.
"They are probably safe but you never know, McLeish is a very capable manager. He's had some criticism from fans but has handled it very well," Ferguson said.
"I've known him since he was a little kid. He was always a very receptive and intelligent young man. He was a great player and had a good career. He did a great job for Scotland and at Birmingham, and will do a good job at Villa given time."
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