On only his second appearance since his shock retirement U-turn, the 37-year-old tapped home Wayne Rooney's cross-shot at the far-post in first-half stoppage time to give the hosts a priceless lead after Rooney had seen his penalty saved by Adam Bogdan.
After a frustrating second-half, Danny Welbeck and Michael Carrick eventually sealed victory late on, ensuring United now only trail neighbours Manchester City, who do not play until Monday, on goal difference.
After Thierry Henry's matchwinning effort for Arsenal on Monday, it was perhaps destined that Scholes would come up with something special once he was confirmed as a member of the United starting line-up.
Had referee Peter Walton not been feeling charitable, it could easily have been a red card, for Scholes' thigh-high assault on Mark Davies was pretty poor in a week when refereeing inconsistencies within the English game have been a talking point.
However, after a couple of cracking long-range shots, Scholes saved the drama until first-half stoppage time.
Having peeled away to the far post, he was perfectly placed to turn home a Rooney cross-shot, which Danny Welbeck had failed to get a touch to.
It was the 151st United goal of Scholes' career, and his first since August 2010, meaning he has equalled last season's tally in just two appearances after abandoning his job coaching the club's reserve team.
It was tough luck on the visitors, particularly their goalkeeper Bogdan, who had performed heroics up to that point to keep the hosts out.
Beaten from 92 yards by Everton goalkeeper Tim Howard on his last league outing, Bogdan got the better of Rooney from 12 yards.
When Zat Knight was beaten to Antonio Valencia's through ball by Welbeck, the Bolton defender pushed his opponent in a desperate attempt to reach the ball.
There was no debate about the penalty. However, as at Manchester City last week, Rooney's spot-kick was saved.
And on this occasion, after plunging to his right, Bogdan got enough on the ball to steer it away from any possible rebound.
The young keeper's place is at risk as Jussi Jaaskelainen nears a full recovery from a thigh strain.
But he must have been pleased with his fine personal display, in particular two saves to deny Welbeck.
And with Mark Davies bundling a Rooney header off the line, Bolton were gaining in confidence, although the ease with which United got behind them explained why USA defender Tim Ream was in the stands, pending his arrival as Chelsea-bound Gary Cahill's replacement.
Bolton wasted an excellent opportunity to equalise straight after the restart when United's defence, not for the first time, got themselves into a tangle, which allowed Davies to race into the area.
He found Ngog but with an unmarked Martin Petrov screaming for a lay-off, the former Liverpool man scooped his shot high over the bar.
This was a warning for Sir Alex Ferguson's men, although there was no immediate end to the chances being wasted.
Rooney was again the culprit just after the hour, when Valencia burst into the box and crossed low to the far post.
In fairness to the striker, he was at full stretch as he went to turn the ball into an empty net and failed in his quest as the ball flashed narrowly wide.
If Bolton's earlier effort was a warning, Gretar Steinsson's was a heart-stopper as his flicked header from a Bolton corner looped over Anders Lindegaard.
Thankfully for the hosts, Rafael had not left his station by the far post and, just as Davies had done from exactly the same position in the first-half, ensured the goal was not breached.
United's second arrived 15 minutes from time, with Welbeck prodding his eighth goal of the season beyond Bogdan after reaching Rooney's lay-off ahead of Sam Ricketts.
The striker took a kick on the back of the leg for his pains, though, and had to be replaced by Javier Hernandez.
But it failed to interrupt the hosts' momentum and, after striding onto Giggs' square pass, Carrick curled a superb left-footed shot past Bogdan from 25 yards.
After successive defeats, it was just what United needed as a confidence booster ahead of a tough sequence of fixtures, starting at Arsenal next weekend, which are likely to determine their chances of retaining the title.
Man Utd: Lindegaard, Rafael Da Silva, Ferdinand, Evans, Evra, Valencia, Carrick, Scholes (Giggs 69), Nani (Park 69), Rooney, Welbeck (Hernandez 78).
Subs Not Used: De Gea, Berbatov, Fabio Da Silva, Pogba.
Goals: Scholes 45, Welbeck 74, Carrick 83.
Bolton: Bogdan, Steinsson, Wheater, Knight, Ricketts, Eagles (Riley 69), Reo-Coker, Muamba (Pratley 80), Petrov (Sanli 88), Mark Davies, Ngog.
Subs Not Used: Lynch, Kevin Davies, Klasnic, Boyata.
Att: 75, 444
Ref: Peter Walton