Sauber and team principal Monisha Kaltenborn parted ways as the Formula One team dismissed reports they treated their drivers unequally.
Kaltenborn, 46, became the first female team principal in F1 when she took over at Sauber in late 2012, while she was also the chief executive officer.
But the team announced her departure on Wednesday, citing a disagreement over the approach for the future.
"Longbow Finance SA regrets to announce that, by mutual consent and due to diverging views of the future of the company, Monisha Kaltenborn will leave her positions with the Sauber Group effective immediately," Sauber chairman of the board Pascal Picci said in a statement.
"We thank her for many years of strong leadership, great passion for the Sauber F1 team and wish her the very best for the future.
"Her successor will be announced shortly; in the meantime we wish the team the best of luck in Azerbaijan."
Earlier reports had suggested the team's owners wanted to give preferential treatment to Marcus Ericsson over Pascal Wehrlein.
But Picci denied those claims, saying they were untrue and detrimental to Sauber's two drivers.
"The owners and board of Sauber Motorsport AG take strong exception to speculative and widespread media reports today that our race drivers have not been, and are not being, treated equally," Picci said.
"This is not only patently untrue, it would be contrary to the team's absolute and longstanding commitment to fair competition.
"These reports, attributed to anonymous "sources", are highly detrimental to both Marcus Ericsson and Pascal Wehrlein as well as to the management and all staff of the Sauber F1 Team."
Sauber have collected just four points this F1 season to be sitting ninth in the constructors' championship ahead of the Azerbaijan Grand Prix.