Hertha scored through Vedad Ibisevic with the Bosnian volleying in for his ninth goal and his first since November, with Bayern, who crushed Arsenal 5-1 in the Champions League in midweek, lacking any game plan despite controlling possession.
The Bavarians, who looked a shadow of the team that obliterated Arsenal with three goals in 10 minutes, had few clear-cut chances in the second half.
But Lewandowski was in the right place at the right time to fire in from close range for his 16th league goal in the sixth minute of stoppage time after Arjen Robben had seen his shot blocked.
"The team is always there when needed," said captain Philipp Lahm. "But to be honest we had come to Berlin to win."
Bayern, who have now won just one of their last three league games, moved up to 50 points with RB Leipzig, in second place on 42, travelling to Borussia Moenchengladbach on Sunday.
"We worked at it until the very end," said Bayern's Thomas Mueller. "We have the mentality but we would have liked to win here."
Borussia Dortmund rebounded from their midweek Champions League loss at Benfica to ease past VfL Wolfsburg 3-0 and climb into third place on 37 points.
An own goal from Jeffrey Bruma put them in the driving seat before Lukasz Piszczek and Ousmane Dembele increased their lead with second-half goals.
Hoffenheim joined them on 37 points after their 2-0 victory over bottom side Darmstadt 98, courtesy of Andrej Kramaric's brace.
Eintracht Frankfurt squandered their chance to go third in the standings, slumping to a 2-0 defeat by visitors Ingolstadt to drop to fifth on 35 points.
Struggling Hamburg SV's Aaron Hunt went from hero to villain after putting them ahead before missing an 86th-minute penalty in their entertaining 2-2 draw against Freiburg.
Hamburg failed to make it three wins in a row but the point was enough to keep them just above the relegation zone.
(Reporting by Karolos Grohmann, editing by Ed Osmond and Toby Davis)
