Substitute Berbatov tapped in from close range after 88 minutes to send Alex Ferguson's team five points clear at the top and earn sighs of relief from his side, who had been reduced to 10 men after the dismissal of Jonny Evans.
Arsenal staged a fightback from two goals down at the Hawthorns but could not find a late winner of their own.
Goals by Andrei Arshavin and Robin van Persie in the last 20 minutes cancelled out strikes by Steven Reid and Peter Odemwingie, who capitalised on a blunder by keeper Manuel Almunia.
United have 63 points from 30 matches while Arsenal are on 58 with a game in hand. Third-placed Manchester City (53) and Chelsea (51), in fourth, meet at Stamford Bridge on Sunday.
Watched from the Old Trafford stands by Ferguson, who was serving the first of a five-match touchline ban for improper conduct, United went a man down after Evans, the Northern Ireland defender, was shown a red card in the 76th minute for a bad tackle on Bolton's American midfielder Stuart Holden.
The leaders were already suffering a defensive crisis with first-choice centre backs Nemanja Vidic and Rio Ferdinand injured, but they did not let the latest setback bother them.
Bolton pushed them hard but the visitors were undone when Jussi Jaaskelainen spilled a shot by Nani and Berbatov converted the rebound for his 20th league goal of the season.
As they have done often this season, United had secured the points without playing particularly well.
"The players deserve all the credit they get," Ferguson told Sky Sports.
"You've got to remember, the last five games we've had two European ties against Marseille, (and games against) Chelsea, Liverpool and Arsenal -- it's a hell of a programme. They've come through it."
SPIRITED ARSENAL
Arsenal's confidence had been crushed recently after losing the League Cup final and tumbling out of the Champions League and FA Cup, but they produced a spirited second-half performance against West Brom.
Arsene Wenger's side got off to the worst possible start when they left Reid unmarked and the West Brom defender jumped to head in Chris Brunt's corner in the third minute.
It got worse after halftime when a mix-up between Almunia and defender Sebastien Squillaci allowed Odemwingie to slide the ball into an open goal.
The visitors gave themselves hope after 70 minutes when Arshavin smashed the ball into the top corner from just outside the area, and the comeback was completed eight minutes later when Van Persie's shot was deflected in by Abdoulaye Meite.
"Of course (we're) disappointed that we dropped two points but it was psychological for the rest of the season -- it was important for us to show character and not lose the game," Wenger said.
In other games, fifth-placed Tottenham Hotspur endured a frustrating time in front of goal as West Ham United held the Champions League quarter-finalists 0-0 in an entertaining encounter at White Hart Lane.
Everton climbed to eighth with a 2-1 victory at home to Fulham in the late game after Louis Saha scored against his former club in the 49th minute following Seamus Coleman's first-half opener.
Fulham pulled one back through Clint Dempsey but the hosts held on.
Stoke City thumped Newcastle United 4-0, while Wigan Athletic scored deep into stoppage time to beat fellow relegation battlers Birmingham City 2-1 at the DW Stadium.
Wigan stayed bottom on 30 points but there are only three points between them and 13th-placed Blackburn Rovers, who came back from two goals down to draw 2-2 with Blackpool.
Wolves are third from bottom after beating West Midlands rivals Aston Villa 1-0 at Villa Park, where home fans held up a banner reading "Had enough, Houllier out" as defeat for Gerard Houllier's team left them one point above the relegation zone.
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