Schalke rallied to edge Aachen, who took a 17th minute lead courtesy of Vedad Ibisevic.
But Rafinha's penalty six minutes later and Aachen captain Moses Sichone's own-goal in the 74th gave Schalke the victory.
In another game, Hamburger SV played to its 12th draw of the season, 1-1 at home to Energie Cottbus, and fell to the bottom of the standings. Hamburg have won only once in 19 games.
Juan Pablo Sorin started the ball rolling for Hamburg by converting a fourth-minute penalty. But Sergiu Radu equalized after a lucky bounce and Hamburg never recovered, although Colin Benjamin hit the post one minute later.
Hannover got two goals from Brazilian Vinicius in the first 37 minutes and another from fellow defender Frank Fahrenhorst before Jan Rosenthal and Altin Lala completed a 5-0 rout of Hertha Berlin.
Leon Andreasen, who transferred to Mainz from Bremen during the winter break, gave his new team their second consecutive victory by converting a penalty in the 61st against Borussia Dortmund. The win moved Mainz off the bottom of the table.
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