Jonker, who joined Bayern Munich in 2009 as assistant coach to fellow Dutchman Louis van Gaal, took charge of the Bavarian club after the head coach was sacked in 2011.
"Although we regret this step, we have had a very good working relationship and gave Andries the chance to take over this task," Wolfsburg sport director Klaus Allofs told reporters on Monday.
"For him it is a unique opportunity to be solely responsible at an international club."
The 51-year-old, who was also Barcelona assistant coach in 2002 also with Van Gaal, coached Bayern's first team before taking over the reserve side in 2011.
He joined Wolfsburg as assistant coach in 2012.
(Reporting by Karolos Grohmann, editing by Ed Osmond)
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