United had lost their previous two league games and there were some jitters when Wayne Rooney's early penalty was saved but Scholes' effort at the end of the first half was followed by goals from Danny Welbeck and Michael Carrick as United moved alongside City on 48 points.
Tottenham Hotspur squandered the chance to make it a three-way tie at the top when they could only draw 1-1 at home to lowly Wolverhampton Wanderers. The North London club stay two points behind the leaders on 46.
Croatian Luka Modric equalised for Tottenham after Steven Fletcher had given Wolves a surprise lead.
City, who play at bottom club Wigan Athletic on Monday, retain top spot from United on goal difference.
Frank Lampard scored the winner for fourth-placed Chelsea (40 points) in a 1-0 defeat of Sunderland but Liverpool, in sixth (35), were frustrated in their quest for Champions League qualification when they drew 0-0 at home to Stoke City.
At the bottom, Blackburn Rovers climbed out of the relegation zone with a 3-1 victory at home to Fulham despite playing more than half the match with 10 men after Aiyegbeni Yakubu was given a red card for a rash tackle.
The 37-year-old Scholes, who provided one of the season's most unexpected turns when he came out of retirement to play in the FA Cup win against Man City last week, scored in first-half stoppage-time - his first goal since August 2010.
Former England midfielder Scholes, who announced he was hanging up his boots at the end of last season when he managed just one goal, was stationed in central midfield but popped up in the area to turn in Rooney's cross to break the deadlock.
GOAL INSTINCT
"It was a bit of a surprise to see [Scholes] pop up at the back post, because at his age and just having come back," manager Sir Alex Ferguson told Sky Sports.
"We had asked him to control the midfield but he has an instinct and always had the instinct for a goal and that could be an important one for us."
Carrick said it was a huge boost to have Scholes, a veteran of numerous title run-ins back for the coming months.
"He's such a world class player and I've learnt so much off him, as well as other players. Being in my position, I've watched him a lot and learnt off him and tried to add his attributes to my game. It's great to have him back and it's given everyone a lift," he told MUTV.
Even after Scholes had given them the lead, however, Bolton occasionally threatened to draw level but United eventually eased to victory and heap some pressure on City's trip to Wigan.
Welbeck made it 2-0 when he poked the ball past Adam Bogdan from Rooney's pass, although the striker appeared to hurt his knee in the process of scoring his eighth goal of the season and was substituted. Carrick's cool finish wrapped up the points.
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