Neuer suffered the injury as Cristiano Ronaldo completed his hat-trick in Real Madrid's dramatic 4-2 extra-time victory over Bayern, which eliminated Carlo Ancelotti's men from the Champions League quarter-finals by a 6-3 aggregate margin.
Bayern chairman Karl-Heinz Rummenigge told reporters Neuer was facing an eight-week absence and on Thursday Bayern released a statement to say the fracture to the 31-year-old's left foot would leave him with no further part to play in their bid for a domestic double.
"Of course I am sad that I will not be available to the team for the season finale," Neuer told his club's official website.
"Now I am concentrating on getting back to health as soon as possible. This is the most important thing for me now."
Neuer missed three games earlier this month due to a foot injury, with Sven Ulrich deputising and the 28-year-old is now set to return for Saturday's home match against Mainz.
Bayern boast a commanding eight-point lead over RB Leipzig at the top of the Bundesliga and face rivals Borussia Dortmund in the semi-finals of the DFB Pokal next Wednesday.
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