Franck Ribery and Thomas Mueller put Bayern in command with quickfire goals midway through the first half but the game soon changed as Kevin Kuranyi pulled one back for Schalke 04.
Bayern had Hamit Altintop sent off in the 41st minute after being booked twice in six minutes but the Bavarians held out comfortably in the second half against uninspired opponents to go a point clear at the top.
"We didn't give them a single chance in the second half and created some ourselves," said Bayern coach Louis van Gaal, whose team also won 1-0 at Schalke in a German Cup semi-final 10 days ago.
"We're leading the table and we still have a chance in three competitions, that is unbelievable,"
Bayern stunned the 61,000 crowd in Gelsenkirchen in the 25th minute when Ribery stroked a low shot into the left-hand corner after the ball was headed into the Frenchman's path by Bastian Schweinsteiger following a cross from the left.
Incredibly, Schalke then lost possession from the kick-off as Altintop stole the ball off Rafinha and slipped it to Ivica Olic, scorer of the winner in Tuesday's 2-1 Champions League defeat of Manchester United.
Kuranyi continued to make life uncomfortable for Germany coach Joachim Low by rising unchallenged to head in Rafinha's cross five minutes later and pull Schalke back into the game.
Low, who vowed never to pick Kuranyi again after the Brazilian-born striker stormed out of the squad in 2008, has come under increasing pressure to reconsider and select him for the World Cup after the player's recent scoring run.
