Gotze, 27, has been restricted to just five league games for the German giants this season as manager Lucien Favre's preferred system left the 2014 FIFA World Cup winner on the periphery of the squad.
"Right now, we are playing 3-4-3," Favre said before their 2-0 win over Wolfsburg, with Gotze named on the bench.
"So, I have been talking to Mario, and unfortunately this is not the right system for him. You must say the truth about this."
With 201 appearances since graduating from the club's academy, the five-time Bundesliga winner is widely considered as a club icon, but with the club not able to offer assurances of first-team football, they've decided to part ways.
"We will part ways with Mario this summer. It was a mutual and respectful decision. He's a great man," sporting director Michael Zorc told the club's official website.
