Ecclestone is set to face trial on bribery charges in Munich in April.
He is alleged to have given a 45 million Euro bribe to German banker Gerhard Gribkowsky in order that Formula 1 would be sold to a private equity group of Ecclestone's choice.
Ecclestone admits paying the money but insists he was blackmailed by threats to reveal false details of his tax affairs.
German media company Constantin Medien claims it lost out financially when a share belonging to German bank Bayern Landesbank, of which Gribkowsky was a board member, was sold to CVC in 2006.
Gribkowsky was convicted of tax evasion, bribery and breach of fiduciary trust in June 2012 and sentenced to eight and a half years in prison.
Ecclestone will continue to run the sport on a day-to-day basis but will do so under greater scrutiny from the company board.
'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,' read a statement.'
'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, Peter Brabeck-Letmathe, and Deputy Chairman, Donald Mackenzie.'