The first leg had ended in a 1-1 draw.
"Unfortunately, during my short eight week tenure I have found an organisation in which the shareholders are not aligned in a common interest, nor have a shared vision for the future of the club," the 53-year-old said in a statement.
"I feel extremely disappointed to have to step away from this great opportunity...
"I truly hope that the shareholders of this club find a solution that allows its fans the opportunity to see this club back where it belongs at the top of German football."
(Reporting by Aditi Prakash in Bengaluru; Editing by John O'Brien)
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