The reigning champions Bayern made hard work of overcoming Ingolstadt, but Carlo Ancelotti’s eventually triumphed 3-1 to move two points clear at the top of the table.
It was Rafinha who sealed the win after the visitors had missed a hatful of chances to equalise.
Inglostadt stunned the home faithful by taking the lead after only eight minutes. Dario Lezcano met Mathew Leckie’s cross to fire past Manuel Neuer, the first man to do so this season.
He went close to adding a second moments later before his sloppy finishing was punished by Robert Lewandowski who equalized with a brilliant chipped effort.
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The Bavarians were lacking their usual intensity as they allowed Leckie the another chance that he fired over before he forced Neuer into a save again before half time.
Xabi Alonso then produced a thunderous strike from outside the area shortly after the restart after Franck Ribery had recorded his second assist of the match.
Leckie was again denied by Neuer and Lukas Hinterseer fired wide when clean through on goal before Ribery claimed a hat-trick of assists to set up Rafinha for the final goal.
Ancelotti said afterwards: "Sometimes we need to suffer.
Dortmund recorded their second successive 6-0 win – and they did it without the benched Mario Gotze, Pierre-Emerick Aubameyang, and Marc Bartra against Darmstadt.
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Despite the thumping scoreline, Dortmund only led by one at the break thanks to Gonzalo Castro.
Adrian Ramos doubled the lead prior to Christian Pulisic notching for his first of the season a day prior to his 18th birthday.
Dortmund's task was made easier when Peter Niemeyer was shown a second yellow card midway through the second period as Castro claimed his brace.
Sebastian Rode added the fifth and Emre Mor concluded the scoring in the dying minutes.
Dortmund boss Thomas Tuchel said: "We controlled the game in every respect and gave our fans a great afternoon.