Manchester United, Manchester City, Chelsea, Liverpool, Arsenal, Tottenham Hotspur, Real Madrid, Barcelona, Atletico Madrid, Juventus, Internazionale and AC Milan are the 12 founding members of a proposed breakaway tournament, which was announced on Sunday.
However, after Borussia Dortmund and RB Leipzig, two of the contenders for the 20-team tournament, which will have 15 permanent members and five qualification places, voiced their opposition to its creation, Bayern announced they would not be joining.
"FC Bayern Munchen has a clear stance on the issue of the Super League," a Bayern statement read.
Bayern president Herbert Hainer added: "Our members and fans reject a Super League. As FC Bayern, it is our wish and our aim that European clubs live the wonderful and emotional competition that is the Champions League, and develop it together with UEFA. FC Bayern says no to the Super League."
CEO Karl-Heinz Rummenigge also said: "On behalf of the board, I would like to make it explicitly clear that FC Bayern will not be taking part in the Super League.
"FC Bayern stands in solidarity with the Bundesliga. It always was and is a great pleasure for us to be able to play and represent Germany in the Champions League.
"We all remember fondly our 2020 Champions League victory in Lisbon -- you don't forget such a joyful moment. For FC Bayern, the Champions League is the best club competition in the world."
PSG have also voiced their disagreement with the creation of the competition.
"Paris Saint-Germain holds the firm belief that football is a game for everyone," a statement from club president Nasser Al-Khelaifi read. "I have been consistent on this since the very beginning.
"As a football club, we are a family and a community whose fabric is our fans -- I believe we shouldn't forget this. There is a clear need to advance the existing UEFA competition model, presented by UEFA yesterday [Monday] and concluding 24 months of extensive and collaborative consultation across the whole European football landscape.
"We believe that any proposal without the support of UEFA -- an organisation that has been working to progress the interests of European football for nearly 70 years -- does not resolve the issues currently facing the football community, but is instead driven by self-interest.
"Paris Saint-Germain will continue to work with UEFA, the European Club Association and all stakeholders of the football family - based on the principles of good faith, dignity and respect for all."
Many of the European Super League clubs suggested in a statement they would continue to participate in their domestic leagues, but all relevant local federations have threatened them with expulsion should the tournament go ahead.