Arjen Robben, the champions' best player this season, struck twice after Ivica Olic had put them in the lead in the 20th minute and Adrian Ramos had equalized for the Berliners on the hour.
Bayern, who finished on 70 points, five ahead of second-placed Schalke 04, are still in the running for an unprecedented treble for a Germany team, playing in the German Cup final on May 15 and the Champions League final a week later.
Dutchman Mark van Bommel became the club's first foreign captain to lift the Bundesliga trophy, in front of 75,000 spectators in the Olympic stadium, before he and his teammates chased coach Louis van Gaal around the pitch to pour beer on him.
Van Gaal, a renowned disciplinarian, tried to outsprint them, then gladly obliged and waved to the fans.
In a contrast of emotions, Hertha players quickly left the pitch after a disastrous season, with several of them set to leave and with fans in no mood to bid them farewell.
Schalke drew 0-0 at Mainz but had already secured the second spot and will compete in next season's Champions League. Werder Bremen clinched the Champions League qualification spot after drawing 1-1 with Hamburg SV to finish third on 61 points.
The result left frustrated Hamburg, in seventh place, outside the European spots, with VfB Stuttgart, in sixth place, grabbing the last available place.
Hosts VfL Bochum slumped to a 3-0 defeat to Hanover 96 and will join Hertha on the way down.
Nuremberg finished third from bottom and will play a relegation playoff with the third-best second division team.
