The Bavarians emerged narrow victors thanks to the midfielder's 75th goal, but they didn't have it all their own way on Saturday afternoon.
With a 2-1 win at Hoffenheim on Saturday, Bayern Munich stretched its unbeaten run in the Bundesliga to 36 matches, equaling the record set by Hamburg between 1982 and 1983.
Niklas Sule gave the hosts the lead in the 34th minute following a mistake from Manuel Neuer. However, Bayern equalised in fortuitous fashion five minutes later when Franck Ribery's free kick was deflected in by Mario Mandzukic for his eighth league goal of the season. With minutes remaining, Thomas Muller netted the winner.
The victory means Bayern climb back to the top of the table and set a new club record for longest unbeaten streak to start a Bundesliga season, surpassing the old mark of 10 matches set at the start of the 1968-69 campaign.
Hoffenheim made one change from last week's win at Hannover, as Kevin Volland replaced Eugen Polanski, while Dante and Javi Martinez returned for Bayern after respective ankle and groin injuries.
After a quiet opening period, Philipp Lahm and Muller were both denied by Hoffenheim goalkeeper Koen Casteels. Lahm was kept out at the near post from the tightest of angles in the 15th minute before the Belgian flung himself to his left to parry Muller's powerful drive from the edge of the area.
The visitors began to dominate possession, but despite their dominance, the hosts took the lead following a mistake from Neuer. The Germany international made a mess of what should have been a routine catch from Kai Herdling's shot from the left-wing and Sule made no mistake when presented with an empty net from six yards out.
Hoffenheim’s lead did not last long, however, as Ribery's free kick took a wicked deflection off Mandzukic and wrong-footed Casteels on its way into the bottom left-hand corner.
The home side nearly equalized through Volland twice in quick succession at the start of the second half but both long ranged efforts were parried by Neuer.
Muller then scored what proved to be the winner from close range after being set up by a quick turn and pass from Ribery.
The French forward then wasted a golden opportunity to add a third goal four minutes from time when he headed Schweinsteiger's cross wide from six yards, but it mattered little as Bayern held on to extend their incredible unbeaten run.