Danny Welbeck and Michael Carrick netted in the second half, the latter with a fine 30-yard effort, as the hosts triumphed despite a penalty and open-goal miss from Wayne Rooney
Adam Bogdan pulled off a remarkable first-half penalty save from Wayne Rooney after Zat Knight felled Welbeck, but Scholes re-opened his professional account on the stroke of halftime with a cool finish.
Welbeck buried an overdue second on 75 minutes but was injured in the process before Carrick's fine placed effort from 30 yards out in the 83rd sealed the victory.
With 20 minutes gone, Knight upended Welbeck in the area for a clear penalty to United, the only surprise being that he received only a yellow for denying a clear goalscoring opportunity. Rooney stepped up confidently but Bogdan heroically sprang to his right to turn the spot-kick behind.
The young keeper proved his mettle again soon after when Welbeck let fly from range having cut inside from the left flank. A low dive allowed the Hungarian to push the shot past the woodwork.
After a scrappy period, Rooney again tested Bogdan, this time from a free-kick curled around the wall, but the ball fell into the youngster’s arms with ease as a half-time stalemate loomed.
The hosts’ talisman was again at fault when he slipped in making the key touch as United put together a thrilling counterattack, his attempted flick into the path of the unmarked Welbeck clumsy and intercepted by the goalkeeper.
Just as it seemed that United would have nothing to show for a dominant half, Rooney picked up a loose ball in the area in stoppage-time and passed across the box where Scholes arrived to dispatch it for the lead.
Early in the second half, David Ngog wasted the first real Bolton chance of the game, lifting a rash shot well from a useful close-range position after Davies had skipped past Patrice Evra on the right flank.
A frustrating afternoon continued for Rooney just after the hour. Antonio Valencia used his pace to get a cross past his marker across the box, with the England man sliding in unmarked at the far post, but he limply diverted it out when it would have been easier to score.
United, who withdrew the excellent Scholes with 20 minutes to go, finally got its second goal in the 75th minute as Rooney, under pressure from defenders, managed to flick it into the path of Welbeck, who buried the chance with no hesitation.
However, in stretching to score, the forward was kicked awkwardly by Sam Ricketts and required immediate substitution by Javier Hernandez as a result.
With the jig up for Bolton, Carrick advanced in the closing minutes to place a 30-yard shot delicately into the bottom-left corner for a rare and very fine goal that underlined the hosts' supremacy.
There might have been a fourth for substitute Ji-Sung Park, threaded through in the box, if not for Paul Robinson's determined last-ditch tackle to deny the Korean late on, with Hernandez then poking into the side netting from a Valencia pass.