Bundesliga leaders Dortmund missed a penalty on their way to a 2-2 home draw against Mainz, allowing Bayern Munich to win the title for the 11th year in a row on goal difference.
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Jamal Musiala scored in the 89th minute to snatch the trophy for Bayern Munich with a 2-1 victory in Cologne on Saturday, the final day of the season.
Dortmund, who took a two-point lead into the final game, needed to win to be sure of ending Bayern's 10-year reign as champions.
However, for the third time in Bundesliga history Bayern managed to jump to first place on the last day of the season, having edged out Werder Bremen in 1986 and Bayer Leverkusen in 2000.
Dortmund fans were celebrating when Cologne's Dejan Ljubicic scored a penalty in the 81st minute to make it 1-1 against Bayern, but Musiala came on as a substitute and scored within four minutes to send the title Bayern's way.
Dortmund had started in pole position, but Sebastien Haller had a first-half penalty saved after Andreas Hanche-Olsen stunned the home fans by heading in Mainz's opening goal in the 15th minute.
Karim Onisiwo then got Mainz's second goal in the 24th with another header and the visitors looked capable of scoring more against the mistake-prone Dortmund defence.
Raphael Guerreiro pulled one back in the 69th minute for Dortmund, but by the time Niklas Sule equalised in the sixth minute of injury time, it was far too late for the "black and yellows".
Bayern announced shortly after winning the title that chief executive Oliver Kahn and sporting director Hasan Salihamidzic were leaving.
Both were under scrutiny for their decision to fire Julian Nagelsmann as coach in March and replace him with Thomas Tuchel, immediately before the team's Champions League and German Cup exits.
Tuchel said on Friday that even a Bundesliga title win would not mask what has been an unsatisfactory season for the Bavarian powerhouse.
Meanwhile, Rani Khedira fired Union Berlin into the Champions League with a late winner over Werder Bremen in a 1-0 victory. Union finished fourth, ahead of Freiburg, who lost 2-1 at Eintracht Frankfurt.
Schalke were relegated after a 4-2 loss at Leipzig, and Stuttgart will contest the relegation/promotion playoff against the team that finishes third in the second division.
Stuttgart drew with Hoffenheim 1-1.
Bochum secured their survival with a 3-0 win over 10-man Bayer Leverkusen.
Australian Associated Press
