Götze, who joined Dortmund as an eight-year-old, killed Thomas Müller's cross adroitly and pinged the ball past a culpable Roman Weindefller with the outside of his right foot in the 66th minute for the opening goal of the game.
Back in the Rhineland for the first time since his €37.5 million summer move, Götze was widely booed, albeit not as toxically as some had predicted, but chose not to celebrate his pivotal goal. Arjen Robben and Müller also struck late on to secure three pivotal points, and Bayern are now seven points clear of Dortmund at the Bundesliga summit.
Dortmund, depleted by the absence of their first-choice back four, will feel aggrieved to have lost their home run in the league so drastically.
Bayern struggled for fluency until Götze's arrival. Pep Guardiola inexplicably started defensive midfielder Javier Martínez in the No.10 role, as the Spaniard delivered an inevitably anonymous display.
Mario Mandžukić, who failed to convert a wonderful Arjen Robben cross in the first-half, was sacrificed in favour of Götze, as Guardiola continued to stamp his Barcelona mark on the Bavarians with the ambivalent strikerless system.
Robert Lewandowski blazed a golden opportunity over inside the opening 10 minutes and Manuel Neuer brilliantly denied Henrikh Mkhitaryan and Marco Reus with the score at 0-1. The scoreline flattered Bayern, themselves without Bastian Schweinsteiger and Franck Ribéry, but their ruthlessness was utterly clinical.