The experienced goalkeeper picked up the problem during Bayern's 5-1 victory over FC Koln last weekend and has now been ruled out of the showdown at Berlin's Olympiastadion.
Although Neuer's recovery has progressed well, the 40-year-old has decided against taking any risks with the World Cup approaching. Bayern confirmed on Friday that their captain would not be available for the final as the club chase another major domestic trophy.
His absence is a significant setback for the German champions, with Neuer remaining one of the most influential figures in the squad despite his age. The veteran has continued to provide leadership and composure in important matches throughout the season.
With Neuer unavailable, 22-year-old Jonas Urbig is set to start in goal for Bayern. The young goalkeeper has already featured 19 times this season and now faces the biggest match of his career.
Bayern will still enter the final as favourites, but Stuttgart will see Neuer's absence as a major opportunity to test an inexperienced replacement on one of German football's biggest stages.
The final also gives Urbig the chance to prove he can handle the pressure of elite-level football while stepping into the spotlight for one of Europe's biggest clubs.