Wimmer previously led Austria Vienna after a spell as interim boss at Stuttgart.
Jahn Regensburg were relegated after finishing bottom of the Bundesliga’s second division this season.
Wimmer’s exit leaves four Premiership clubs seeking a new manager – Dundee, Kilmarnock, Rangers and now Motherwell.
With Heart of Midlothian having taken Derek McInnes from Kilmarnock as their new head coach, at least five of 12 top-flight clubs will start the new season under new management.
Motherwell said Wimmer had “reached out to the chairman and chief executive of the club to inform them that he would like to remain in Germany” and become Jahn Regensburg boss.
“Wimmer explained the reasons for wishing to accept the new role were predominantly due to major family issues that have recently arisen in Germany,” said the club in a statement.
“Following extensive conversations with Michael, the club very reluctantly negotiated a compensation package with SSV Jahn Regensburg.
“The club wishes Michael and his family the best going forward. The club will now start the process of recruiting a new manager with immediate effect. The club will be making no further comment at this time.”
