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.
Bayern, who were without injured Franck Ribery, have now won all games in every competition so far this season and are on 12 points along with promoted Eintracht Frankfurt who beat Nuremberg 2-1 on Friday.
"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.
Schalke, who showed none of the attacking flair that earned them a 2-1 win at Olympiakos in their midweek Champions League group match, imploded following the quickfire goals and failed to threaten the Bayern goal.
Champions Dortmund are five points behind, after Hamburg battled to victory with two goals from South Korea's Son Heung-min.
The hosts needed just two minutes to score when Rafael van der Vaart was given far too much space on the left to cross and Son beat Mats Hummels to head in his second goal of the season.
Dortmund instantly took control, launching a barrage of attacks until half-time but neither Marco Reus nor Robert Lewandowski could beat keeper Rene Adler.
GOAL RUSH
Ivan Perisic did it better, lobbing in the equaliser from the left 21 seconds after the restart. In a frantic five-minute spell, however, the hosts struck twice through Ivo Ilicevic and Son before Croat Perisic cut the deficit on the hour.
Dortmund are on seven points along with fellow Champions League competitors Schalke while Hamburg, who hold the record for the longest unbeaten run of 36 league games from 1983, managed to lift themselves off the bottom after three straight defeats.
"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.
Mainz 05 climbed up to 11th place with a 2-0 home win over
