“That was my last competitive game in charge of Dortmund,” Stoeger told the media after his side’s 3-1 defeat to Hoffenheim on Saturday.
The decision, he continued, had been made “some time ago”, together with the club hierarchy.
“A new impulse with a new coach will be good for the club,” said Stoeger.
Stoeger took over from Peter Bosz last December, and was tasked with guiding Dortmund to a top-four finish and a place in the Champions League.
He completed the task on Saturday, as Dortmund finished fourth despite defeat to Hoffenheim.
OGC Nice manager and former Borussia Moenchengladbach coach Lucien Favre is the favourite to succeed Stoeger.