Heiko Westermann fired home from close range in the 87th minute to give Schalke the points and leave the title run-in a perfectly poised two-horse race with two games left to play.
Bayern fell behind to a Marco Reus goal on the hour but Miroslav Klose headed an equaliser 13 minutes later, keeping them top on goal difference.
Lucas Barrios, who is qualified to play for either Argentina or Paraguay at the World Cup but has yet to be picked by either, hit a hat-trick in Borussia Dortmund's 3-2 win at Nuremberg, taking his tally for the season to 18.
Stefan Kiessling, on the fringes of Joachim Low's Germany squad, scored twice, the second a penalty, in Bayer Leverkusen's 3-0 win over struggling Hanover 96 to take his tally to 21 and overhaul Edin Dzeko as the league's top scorer.
Burkina Faso striker Aristide Bance scored twice to help Mainz 05 draw 3-3 at home to Eintracht Frankfurt, who had raced to a 2-0 lead with an Alexander Meier brace in only 20 minutes.
DISMAL OPENING
Saturday's results left Bayern and Schalke with 64 points from 32 games and guaranteed both teams a place in the Champions League next year.
Bayern host VfL Bochum and visit Hertha in their final two games while Schalke entertain Werder Bremen and then travel to Mainz.
Werder Bremen moved into third spot, which would earn them a Champions League qualifying place, with 57 points, ahead of Leverkusen on goal difference, after a Torsten Frings penalty in stoppage time gave them a 1-0 win over Cologne.
Borussia are a further point behind in fifth place.
Schalke's game came to life in the second half after a dismal opening although it was their lowly opponents who took the initiative, with Cicero having a shot kicked off the line.
Schalke, who prefer to let their opponents do the work under Felix Magath's leadership, then snatched a winner with a South American-made goal.
Uruguayan substitute Vicente Sanchez crossed from the left and found Peru's Jefferson Farfan, whose header was saved by Jaroslav Drobny only for Westermann to stab home the rebound.
Schalke striker Kevin Kuranyi, whose recent scoring form has put pressure on Low to recall him, had an unhappy game, missing two good chances.
Klose, one of Low's favoured strikers, notched only his third goal of the season to rescue a point for Bayern, heading in a cross from Philipp Lahm.
Reus had opened the scoring after rushing on to United States midfielder Michael Bradley's pass behind the defence and firing past Jorg Butt.
