Stoeger announced his departure immediately after Dortmund's 4-1 defeat to Hoffenheim, reports Xinhua news agency.
"This was my last game at Dortmund's sideline. We have already mutually agreed that a new impulse is necessary and will help the club," Stoeger said on Saturday evening.
Stoeger, who signed a short-term contract until the end of the season, was in charge for overall 19 games. He reaped nine victories, six draws and four defeats.
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