A total of four changes following Thursday's UEFA Super Cup triumph over Sevilla saw Robert Lewandowski, Niklas Sule, Lucas Hernandez and Leon Goretzka dropped to the bench.
Hoffenheim barged into a 16th minute lead from a corner after Ermin Bicakcic redirected the delivery into the far corner despite the best efforts of Alphonso Davies on the opposite end.
The home side got a second on 24 minutes after Munas Dabbur pounced on Benjamin Pavard's defensive error before going clear to chip Bayern goalkeeper Manuel Neuer.
Hoffenheim should've had a third on the brink of the half-hour mark, but Christoph Baumgartner couldn't find the intended target after bursting through Bayern's defence.
The Bavarians managed to cut the deficit when Joshua Kimmich curled in off the underside of the crossbar 36 minutes in following an assist from Thomas Muller.
Croatian Andrej Kramaric should've handed his side a three-goal cushion at halftime, but Neuer pushed his speculative attempt onto the crossbar after twisting and turning in the box.
Bayern almost clawed their way back ten minutes from halftime after a close range attempt from Joshua Zirkzee rattled the crossbar as the hosts began breathing heavily.
The treble champions introduced the big guns following the midway stage in the second half in Lewandowski, Goretzka and the returning Kingsley Coman.
However, Hoffenheim still took the game in their stride in the last 12 minutes and secured a third when Kramaric propped up alone in the area to volley beyond Neuer.
There was no stopping the hosts who piled more misery in stoppage time when Kramaric completed his brace from the penalty spot after Neuer brought down Ihlas Bebou to round off a big win.