Visitors Bayern, fresh from their opening 2-1 Champions League win over Valencia on Wednesday, took the lead in the 55th minute when in-form Toni Kroos - set up by Thomas Muller - curled a low shot from 14 metres past keeper Lars Unnerstall.
Muller then scored the second goal himself, threading the ball through the legs of defender Christian Fuchs on the right and slipping a shot between two others for his fourth goal of the season to silence the 61,000 crowd at the Auf Schalke Arena.
"We saw a very intense match from both teams and Schalke stood up very well especially in the first half," said Bayern coach Jupp Heynckes.
"We showed our class in the second half, dominated and deserved to win.
"It is good news that we have opened up a five-point lead [over Dortmund] but the championship is a long marathon of 34 games," he said.
Champions Dortmund are five points behind, after Hamburg battled to victory with two goals from South Korea's Son Heung-min.
"The game was a real show," said Dortmund coach Jurgen Klopp. "We had problems pushing through our game at the beginning and Hamburg were clever, taking their few chances well."
VfL Wolfsburg's Emanuel Pogatetz scored a curious own goal in their 1-1 draw at home to Greuther Fuerth when he failed to clear a deep kick from Greuther keeper Max Gruen and connected with the ball to send it past his charging keeper Diego Benaglio.
Ivica Olic levelled three minutes before the break after Thomas Kahlenberg's shot hit the bar and bounced towards the Croat, who had no problem heading it in from five metres out.
