Bayern made it 10 victories out of 10 in all competitions this year after twice coming from behind to beat fourth-from-bottom Fortuna.
Defender Jerome Boateng nodded the winner in the 86th minute, his first goal since joining the club in 2011.
First-half goals from Julian Draxler and Klaas-Jan Huntelaar secured Schalke's victory over champions Dortmund and elsewhere there were spectacular goals and a double dose of controversy.
VfL Wolfsburg produced the day's best goals as they came from behind to win 5-2 at Freiburg.
"The penalty should not have been given," he told reporters. "But I have to also say that I no longer know when a penalty should be given and when a penalty shouldn't be given."
There was also confusion early in Borussia Monchengladbach's 1-1 draw at home to Werder Bremen when the referee awarded a goal to Patrick Hermann for the hosts and then disallowed it for offside after consulting his assistant.
Schalke, who won the season's first Ruhr derby by the same score, climbed into the Champions League play-off berth in fourth spot on 39 points. Mainz, two points behind in sixth, also stayed in the hunt.
Dortmund's usually effervescent coach Jurgen Klopp was left almost speechless by the defeat against Schalke.
"We lost 2-1, what can I say?" he told Sky Sports. "Everyone in our team understands what a derby means."
Asked what it meant to lose two derbies in a season, he replied: "I have no words for that," and walked off.
Draxler swept home Atsuto Uchida's low cross from the right in the 12th minute as Schalke tore into their arch rivals.
