The visitors looked like causing an upset thanks to an Alexander Esswein first half goal, but the Polish striker drew his side level before the German netted a penalty
Thomas Muller grabbed a late winner from the penalty spot as Bayern Munich came from behind to edge out Augsburg 2-1 on Saturday.
The defending Bundesliga champions had fallen behind to an Alexander Esswein strike shortly before the interval, but hit back through Robert Lewandowski and Germany international Muller.
Augsburg came into the fixture having won two of their last three matches against Bayern, although both of those triumphs came after Pep Guardiola’s men had wrapped up the league title.
That impressive record enabled the away side to play with a degree of confidence and Esswein’s opener set alarm bells ringing.
Bayern pressed for an equaliser, bringing Kingsley Coman on for a first appearance since his deadline-day switch from Juventus, and their persistence paid off when Lewandowski looked to have salvaged a point 13 minutes from time.
But Augsburg’s hard work was completely undone in the 90th minute – Muller netting from the spot after Markus Feulner was harshly ruled to have brought down Douglas Costa in the box, preserving Bayern’s 100 per cent start to the season.
Mario Gotze was left out of the Bayern squad after picking up a knock, while, with Arjen Robben injured on international duty, Guardiola included Rafinha, pushing Philipp Lahm out wide, and brought Jerome Boateng in for Juan Bernat.
Lacking the creativity of Robben on the wing, Bayern struggled to carve out any clear-cut opportunities in the early stages, with Lewandowski’s eighth-minute cross drifting just out of the reach of Muller.
Bayern had to wait until the 21st minute to test Marwin Hitz with the Augsburg goalkeeper diving to his right to keep out a close-range header from Thiago.
Despite dominating possession, the hosts posed little threat to the Augsburg goal as the half progressed, and they were punished two minutes from the break when Esswein capped a neat passing move by prodding beyond Manuel Neuer from 18 yards with the outside of his right boot.
Koo Ja-cheol and Raul Bobadilla both had hands in the build-up, with the former eventually providing the assist for an unmarked Esswein to fire home.
David Alaba sent an optimistic effort high and wide as Bayern desperately pushed to restore parity early in the second half, before Thiago scooped a half-volley over from a central position.
Coman was handed his debut as a 55th-minute replacement for Arturo Vidal but, despite predictions from sporting director Matthias Sammer that the teenager would “explode into life” if given the opportunity, he showed few signs of being able to transform Bayern’s fortunes.
Hitz was equal to a Xabi Alonso free-kick from 25 yards shortly after the hour mark, but he was cruelly beaten by Lewandowski for the leveller.
Lewandowski weaved his way through the Augsburg defence before offloading left to Muller, whose shot from a narrow angle was blocked by Hitz. The ball fell kindly for Lewandowski on the rebound and he was left to tap in to an open goal from close range.
Muller completed the turnaround in the final minute, sparing Bayern’s blushes from 12 yards.