Winger Arjen Robben scored twice as Bayern, undefeated in the league this season, outlasted Augsburg, who managed to keep pace for almost an hour before running out of steam.
"It is not always easy after a Champions League game but we did it very well today," said Bayern coach Pep Guardiola, whose team beat CSKA Moscow in midweek.
The Spaniard played down clinching the unofficial autumn championship which means they are top until the season resumes in January.
"Autumn champion only means we have won many games. But it means nothing more than that," said Guardiola.
Defender Mehdi Benatia headed in his first Bundesliga goal in the 58th after Bayern completely dominated the Bavarian clash but wasted chance after chance.
Earlier, Franck Ribery fired wide with only Alex Manninger to beat and the goalkeeper also denied Robben.
But the Dutchman, in sensational form throughout 2014, curled in a trademark left-foot shot off the post in the 59th to sink Augsburg, who snapped Bayern's unbeaten run last season.
Robert Lewandowski slotted in his seventh goal of the campaign in the 68th and Robben grabbed his eighth with a clever low shot from the edge of the box as the hosts suffered their first loss in five games after four straight wins.
Bayern are on 39 points from 15 games, having won 10 of their last 11 matches, with two left to play until the winter break.
VfL Wolfsburg, in second on 29, meet Paderborn on Sunday while Augsburg stay third on 24.
Last season's runners-up Borussia Dortmund continued their erratic season, losing 1-0 at Hertha Berlin to drop back down into the relegation playoff spot in 16th.
Former Dortmund striker Julian Schieber shook off two defenders to slot in five minutes before the break as Dortmund suffered their ninth loss in 15 matches.
Fellow Champions League club Schalke 04 suffered a similar fate, slumping to a 2-1 loss against visitors Cologne to drop to sixth on 23.
Werder Bremen's talented Davie Selke scored in the 88th minute to rescue a point in their 3-3 draw against Hanover 96. They join Dortmund and Freiburg on 14 points.
(Reporting by Karolos Grohmann, editing by Ed Osmond and Toby Davis)
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