Ecclestone is due to go on trial in Munich in April following allegations he bribed German banker Gerhard Gribkowsky during negotiations relating to the sale of the sport in 2006.
The 83-year-old denies the allegations and intends to continue to run F1 on "a day-to-day basis".
A statement from the holding company of the Formula One Group read: "The board of Delta Topco Limited has met today to discuss the decision of the Munich Court to commence proceedings against Mr Ecclestone.
"Mr Ecclestone has reassured the board that he is innocent of the charges and intends to vigorously defend the case which will commence in late April 2014.
"After discussion with the board, Mr Ecclestone has proposed and the board has agreed that until the case has been concluded, he will step down as a director with immediate effect, thereby relinquishing his board duties and responsibilities until the case has been resolved.
"The board believes that it is in the best interests of both the F1 business and the sport that Mr Ecclestone should continue to run the business on a day-to-day basis, but subject to increased monitoring and control by the board. Mr Ecclestone has agreed to these arrangements.
"The approval and signing of significant contracts and other material business arrangements shall now be the responsibility of the chairman, Mr Peter Brabeck-Letmathe, and deputy chairman, Mr Donald Mackenzie."
Ecclestone was indicted in July over a 44million US dollars (£29million) payment made to Gribkowsky to help smooth the sale of F1 to private equity firm CVC Capital Partners eight years ago.
Ecclestone has previously claimed he was being "shaken down" by Gribkowsky, who was at the time employed as the risk officer at Bayern LB, the German bank overseeing the sale.
Gribkowsky was imprisoned in June 2012 for eight and a half years after being found guilty of breach of trust, tax evasion and receipt of corrupt payments.
Prosecutors in Gribkowsky's trial claimed he sold the stake without updating its valuation in return for bribes disguised as consulting contracts.
Ecclestone has admitted making the payment to Gribkowsky but claims he did so because he had been threatened with blackmail.