Substitute Berbatov tapped in from close range after 88 minutes to the relief of a United side reduced to 10 men after the dismissal of defender Jonny Evans. The Bulgarian's 20th league goal of the season sent Alex Ferguson's team five points clear at the top of the table.
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 international, was shown a red card in the 76th minute for a bad tackle on Bolton's American midfielder Stuart Holden.
Bolton pushed them hard but the visitors were undone when Jussi Jaaskelainen spilled a shot by Nani and Berbatov coverted the rebound.
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.
In other games, fifth-placed Tottenham Hotspu were held to a goalless draw by West Ham United. Wigan Athletic scored deep into stoppage time to beat fellow relegation battlers Birmingham City 2-1 at the DW Stadium. Blackburn Rovers 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.
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