The veteran midfielder, who came out of retirement on Sunday ahead of the FA Cup third round win over Manchester City, opened the scoring for United on the stroke of half-time before Danny Welbeck and Michael Carrick added late goals to make it a comfortable win in the end for Sir Alex Ferguson's charges.
It could have been many more for the home side who were profligate in front of goal and even saw a penalty saved when Wayne Rooney was denied by Adam Bogdan in the 22nd minute after Zat Knight brought down Danny Welbeck in the box.
However, Rooney found Scholes on the edge of the six-yard box for the former England international to slot home in the 45th minute to give United a deserved lead prior to the break.
It took them a while to again break down the Trotters defence, now without Gary Cahill who is set to join Chelsea, but a second goal did come in the 74th minute when Rooney fortuitously prodded through Welbeck who calmly finished despite being under extreme duress from Mark Davies. Both Rooney and Welbeck suffered injuries in scoring the goal making it a very subdued goal celebration indeed with the latter, who netted fifth of the campaign, having to come off straight away with what looked to be a knee problem.
Less than ten minutes later, United were three to good when substitute Ryan Giggs rolled the ball to Michael Carrick who took a touch before placing a curling left-footed shot past Bogdan from 25 yards out to enable the reigning champions to join league leaders City on 48 points at the top of the table ahead of their trip to Wigan Athletic on Monday night.
It was a first loss in three games for Own Coyle's Bolton who dropped to 19th after failing to beat United for the ninth meeting in a row.
TRIBAL ASKS: Man Utd will soon get some key players back which will give them a big boost. Is their experience of winning titles critical to overhaul Man City in the race for the Premiership?
Old Trafford, Manchester - 75,444
Yellow cards:MANU - nil BOL - Zat Knight 21'