On Friday, Bayern announced Neuer was not a part of the 21-man squad making the trip to the German capital for the showpiece event, having failed to recover from injury.
The 40-year-old goalkeeper made a surprise return to Germany's World Cup squad on Thursday, coming back two years after announcing his international retirement to play in a fifth World Cup.
Named man of the match in Bayern's 2-1 win away at Real Madrid in the Champions League quarter-finals in April, Neuer has continued to play at a high level this season but has missed several games through injury.
The 2014 World Cup winner has been troubled by the recurrence of a calf injury in the same leg he broke in a skiing accident in 2022.
Neuer was subbed out with 60 minutes played in Bayern's final Bundesliga game on Saturday with a problem in the same calf muscle.
Neuer will be replaced by understudy Jonas Urbig, who will also accompany the Germany squad this summer as a practice goalkeeper.
Bundesliga winners in mid-April, Bayern can win a record-extending 14th double by beating Stuttgart in the German capital on Saturday.