A late goal from Joshua Kimmich was the difference, as the versatile superstar broke the 2-2 deadlock in the 82nd minute to give Hansi Flick and the Bavarians yet another trophy.
The victory inside an empty Allianz Arena comes on the back of triumphs in the Bundesliga, DFB-Pokal, Champions League, and UEFA Super Cup.
Bayern appeared to have Wednesday's match under control in the opening half after goals from Corentin Tolisso and Thomas Muller. But Julian Brandt got Dortmund back in the contest before the halftime interval, and Norwegian star Erling Haaland equalized in the 55th minute.
The young phenom had a glorious chance to give Dortmund the advantage later in the second half but Manuel Neuer's superb save kept the sides level, setting the table for Kimmich to deliver the decisive blow.
Fortuitous as the redirection off Kimmich may have been, the buildup to the goal - the pressing in midfield and quick interchange of passes - had all the hallmarks of Bayern's dominant run since returning to play earlier this year.