Jerome Gondorf struck a 92nd-minute winner to defeat a Schalke side reduced to 10 men.
Thomas Muller admitted wasteful finishing was responsible for Bayern Munich's goalless draw with Bayer Leverkusen at the Bay Arena.
Bundesliga leaders Bayern Munich were unable to capitalise against 10-man Leverkusen as they finished in a scoreless draw.
Bayern Munich's injury crisis may be worsening as Javi Martinez and Kingsley Coman both limped off in their 0-0 draw at Bayer Leverkusen on Saturday.
Borussia Dortmund defender Sokratis Papastathopoulos dedicated his goal against Eintracht Frankfurt on Saturday to injured teammate Marc Bartra.
Bayern Munich saw their lead at the summit of the Bundesliga reduced to eight points after being held to a goalless draw by 10-man Bayer Leverkusen.