Weidenfeller, who joined from Kaiserslautern in 2002, is Dortmund's longest-serving player and has made 450 competitive appearances.
The DFL has said 45 incorrect calls could have been averted had the video assistant referee system been in place in the Bundesliga this season.
Bayer's claims to being Germany's third-best team are under threat. Tuesday's loss to Atletico signalled what could be the start of a very big slide.
Hermann Gerland and Jochen Sauer will head Bayern Munich's new academy, which is set to open this summer.
Franck Ribery and Jerome Boateng are both stepping up their comeback bids and nearing a return to action for Bayern Munich.
The leading director of the German Football Association's (DFB) coach's training facilities Frank Wormuth believes tactics are "overrated."