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 equalised 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 a treble that has never been won by a German team. They play 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 team mates 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 woeful season, with several of them set to leave and with fans in no mood to bid them farewell.
"I think people will remember the Bayern team of the 2009/10 season," Van Gaal told reporters. "It is wonderful and it is just great that this crowd remained in their seats for the celebrations," he said of the Hertha fans.
"We had the best attack, the best defence and I think we played the most attractive football this season and that is important for me. It is a good to win and we managed to stay in our rhythm. I will party until very late tonight."
SCHALKE SECOND
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.
Claudio Pizarro scored the only Werder goal and equalled Brazilian Giovane Elber's 133 Bundesliga goals, making them the leading foreign goal scorers of all time.
The result left a frustrated Hamburg in seventh place and outside the European spots. VfB Stuttgart, in sixth place, grabbed the last available place.
Hosts VfL Bochum slumped to a 3-0 defeat to Hanover 96 and will join Hertha on the way down, as a few dozen angry Bochum fans tried to storm the pitch.
Nuremberg finished third from bottom and will play a relegation play-off with the third-best second division team.
