The hosts were already labouring badly when Jonny Evans was sent off in the 76th minute for a reckless challenge on Stuart Holden. But after Matthew Taylor failed to take a glorious chance for the visitors, Berbatov pounced for his 21st goal of the season after goalkeeper Jussi Jaaskelainen failed to hold Nani's shot.
Referee Andre Marriner rejected United's appeal for an early penalty when Javier Hernandez's shot bounced onto Gary Cahill's arm.
United goalkeeper Edwin van der Sar got his positioning right to ensure Martin Petrov's curling free-kick did not find the net, and Bolton's Daniel Sturridge then failed to make the most of a half-chance and Johan Elmander fired a thunderbolt straight at Patrice Evra.
Wayne Rooney made a chance for Hernandez but the Mexican could not direct his near-post effort on target. Rooney was off target with a couple of efforts too. Berbatov replaced Hernandez for the second half.
Petrov threatened with a speculative effort from an acute angle, before Berbatov sent a snap-shot narrowly wide. The dismissal of Evans looked to be a blow, while for Bolton the worry was that Holden was taken off on a stretcher. Taylor held his head in his hands as he sent a free header straight at Van der Sar. And when Berbatov tapped home, the feeling of this being a key day in the title battle was inescapable.