Dortmund CEO Hans-Joachim Watzke said in a statement on Monday that both clubs were in agreement about committing to the Champions League. RB Leipzig have also joined Bayern and Dortmund in opposing the plans and Bayern CEO Karl-Heinz Rummenigge said: "FC Bayern has not been involved in the plans for creating a Super League. We are convinced that the current structure in football guarantees a reliable foundation.
"FC Bayern welcomes the reforms of the Champions League because we believe they are the right step to take for the development of European football. The modified group stage will contribute to an increase in excitement and the emotional experience in the competition.
"I do not believe the Super League will solve the financial problems of European clubs that have arisen as result of the coronavirus pandemic. Rather, all clubs in Europe should work in solidarity to ensure that the cost structure, especially players' salaries and agents' fees, are brought in line with revenues, to make all of European football more rational."
Earlier on Monday, Watzke had released a statement which outlined both Dortmund's and Bayern's opposition to the Super League.
"The members of the [European Club Association] ECA board got together on a virtual conference on Sunday evening and reaffirmed that last Friday's board decision remains valid," Watzke had said.
"Both German clubs on the ECA board, Bayern Munich and Borussia Dortmund, represented 100% congruent views in all discussions."
At a news conference on Monday, Bayern coach Hansi Flick said he didn't support the new league.
"I back the club's statement and Dortmund's statement. It would not be good for European football," he said.
Sources have told ESPN that Dortmund were surprised by the statement released by the 12 Super League clubs on Sunday confirming their plans.
Leipzig, who are second in the Bundesliga, have also said they are not interested in joining the breakaway Super League.
"We are advocates of sporting competition," Leipzig CEO Oliver Mintzlaff said. "And sporting competition in professional football means fighting to achieve a position in the domestic league table that allows a team to take part in an international competition. For us, changing this is out of the question.
"We reject any plans to establish a Super League."
As part of the new project, all 12 clubs associated with the league are expected to resign from the European Club Association, the body which brings together 246 major clubs, with immediate effect.
Sources have told ESPN that Arsenal have left with chief executive Vinai Venkatesham stepping down from his position on the ECA board. Venkatesham was only elected last month.
Juventus, AC Milan and Inter Milan have all confirmed their exit with ECA chairman Andrea Agnelli also resigning from his role. Manchester United have stood down with the club's executive vice-chairman Ed Woodward resigning his position as a board member, while sources have told ESPN that Tottenham have left with Chelsea set to follow.
Dortmund CEO Watzke has said in the past that he opposed Super League plans and instead backed those to reform the Champions League, also in order to prevent a breakaway league from happening.
"That decision by the ECA stipulates that the clubs want to implement the planned reform of the UEFA Champions League," Watzke added in his latest statement.
"It was the ECA board's clear opinion that the plans for the foundation of a Super League are rejected."
Dortmund and Bayern were among the three clubs rumoured to join the 12 clubs for the inaugural Super League, which could start for the 2023-24 season or as soon as practicable.
However, Watzke laid emphasis on the fact that neither of the German clubs represented on the ECA were committed to the reforms.