Sammer replaces Nerlinger at Bayern
Nerlinger's exit follows two seasons without a title for the Bavarian giants, who finished second last term behind Borussia Dortmund, who also beat them in the final of the German Cup.
Sammer, 44, captained the German team to the 1996 European title and also won the Ballon d'Or that year. Sammer has been national technical director of the German Football Federation (DFB) since 2008, with a contract that was due to run until 2016.
He also previously coached Dortmund and Stuttgart.