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.
Stefan Kiessling scored twice for third-placed Bayer Leverkusen to join Kuranyi at the top of the scoring table with 18 goals, although his team lost 3-2 to an 89th minute Maik Franz goal at Eintracht Frankfurt.
Bayern lead with 59 points from 29 games and five matches to play, one ahead of Schalke, while Leverkusen, a team who have become famous for fading at the crucial stage of the season, are a further five points behind.
Leverkusen were unbeaten after their first 24 games, a Bundesliga record, but have lost four of their last five.
They are only one point clear of Borussia Dortmund, who beat Werder Bremen 2-1 to close in on a Champions League qualifying spot.
Bottom club Hertha Berlin won 3-0 at Cologne to move within three points of 16th-placed Freiburg, who were held 1-1 at home by VfL Bochum and occupy the relegation playoff place.
LINESMAN PUSHED
"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.
Olic in turn laid the ball off for Mueller to tap into an empty net.
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.
Bayern were under even more pressure thanks to the antics of Altintop. Having been extremely lucky to escape with a booking after he pushed the linesman in a fit of anger over a decision, the Turkish midfielder needlessly tripped Rafinha from behind and was sent off.
Altintop even had the temerity to wave his arms in disgust as he left the field.
