Premier League - Berbatov rescues 10-man United
It turned a frustrating afternoon into a joyous one for United who had Jonny Evans sent-off for a shocking tackle 14 minutes from time.
Despite that setback, and a poor performance, they now find themselves five points clear at the top of the table after Arsenal could only draw at West Brom.
Sir Alex Ferguson, forced to watch the match from the stands due to his five-match touchline ban, must have been tearing his hair out for the majority of the contest as United, on the back of two consecutive Premier League defeats, again struggled to create.
United had plenty of possession in the opening half but for the most part looked devoid of ideas.
They did have a shout for a penalty after 10 minutes when Javier Hernandez's close range effort hit the arm of Gary Cahill although it is hard to know what the Bolton man could have done about it.
Owen Coyle's men didn't create any clear chances themselves but they did look to attack, albeit conservatively, whenever they got the chance.
The vast majority of the second-half was turgid stuff as Bolton comfortably soaked up United's attacks, helped by outstanding performances from their centre-half pairing of Cahill and David Weather.
But then the match took a new twist in the 76th minute when Evans went into a tackle with Stuart Holden studs first.
The tackle ended both men's afternoons, Holden departed on a stretcher, while Evans was given a straight, and merited, red card.
However, that is a problem for another day, if anything the dismissal saw Bolton drop a little deeper which encouraged United to attack despite their depleted numbers.
Rooney and Nani both got shots on target after the red card, but United's ambition was a dangerous game, and Matthew Taylor, on for Holden, really should have given Bolton the lead in the 85th minute but he put a free-header straight at Edwin van der Sar.
Instead it was United, as they so often do, who nicked it at the death as Berbatov was in the right spot to walk the ball in after Jaaskelainen's spill.
The Bulgarian looked to the linesman to make sure he was onside, while Bolton's players complained, but replays showed he was on.
There would be no more drama after that, Bolton were left stunned, United delighted, and if they lift the title in May, this might well be the day they deduce that they won it.