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Thomas Muller has been singled out by returning Bayern Munich boss Jupp Heynckes as a leader within the club.
Aubameyang, last season's Bundesliga top scorer, had been expected to leave Dortmund in the summer.
Germany international Werner had been undergoing tests after suffering "breathing and circulation problems."
Bayern Munich CEO Karl-Heinz Rummenigge says Thomas Tuchel remains in the frame to take over as the club's coach next season.
Earlier this week, a source told ESPN FC that Brooks, 24, was closing in on a return to full training.
Chile, third in the 10-team South American group, need a point to ensure at least a playoff spot.