Dimitar Berbatov struck with two minutes to go as United returned to winning ways in the Barclays Premier League.
The Bulgarian, who has fallen out of favour in recent weeks, climbed over the bench to rescue the Red Devils, who appeared to be labouring to a stalemate.
It was tough on Bolton, who frustrated United for much of the afternoon, restricting them to few chances.
And United looked to be following up defeats at Chelsea and Liverpool with just a point when Jonny Evans was sent off for a challenge that left Stuart Holden writhing in agony.
The three points will be a huge relief to Sir Alex Ferguson, who watched from the stands after starting his five-game touchline ban but kept in touch with coach Rene Meulensteen by telephone.
With attacking line-ups on both sides, the game started at a blistering pace with Fabrice Muamba falling over a good chance from eight yards out and Wayne Rooney blasting just wide from long range.
United then felt they should have had a penalty on 10 minutes when Wes Brown’s far post header dropped for Javier Hernandez whose close range effort appeared to be deflected wide off Gary Cahill’s hand.
Rooney tried another spectacular volley that was well stopped by Jussi Jaaskelainen and then pulled a cross back for Hernandez, who clipped his shot just wide.
Ferguson made a double switch at half-time with Fabio and leading scorer Berbatov coming into the action but United were finding it difficult to break down the well-organised Bolton back-line.
England centre-halves Gary Cahill and David Wheater marshalled the defence superbly and made last ditch tackles to deny Rooney and Berbatov as the frustration inside Old Trafford began to grow.
They finally worked some space in the box in the 73rd minute when Rooney laid the ball off to Berbatov but his curling effort was just off target.
United were reduced to 10 men with 15 minutes to go when Evans was shown a straight red for a challenge on Holden, who was carried off with his team-mates clearly shaken by his injury.
And it almost got worse from the free-kick with Johann Elmander’s strike drifting narrowly wide.
Rooney cut inside to force a desperate save from Jaaskelainen while Matty Taylor wasted a free header as both sides pushed for all three points late on.
And with two minutes to go, United grab the winner when Nani’s shot was spilled by Jaaskelainen and Berbatov scrambled the ball home from two yards.
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