The British businessman is due to stand trial in Munich in April over allegations he bribed former German banker Gerhard Gribkowsky during negotiations concerning the sale of F1 championship rights in 2006.
The 83-year-old magnate has repeatedly denied any wrongdoing and intends to continue to run the sport on "a day-to-day basis".
"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," read a statement from the F1 holding company, Delta Topco Limited.
"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."
Ecclestone is also facing a £90m civil claim in London's High Court brought by German media company, Constantin Medien. They claim they lost out financially when the sport was sold in 2006.
He has admitted paying Gribkowsky, who was jailed for eight-and-a-half years in June 2012 for taking an illegal payment, but disputes the bribery charges, claiming he was the victim of blackmail.
"This is about me proving my innocence," Ecclestone told the Handelsblatt newspaper on Thursday. "That is why I will go to Munich for this trial."
The motor-racing magnate has been under investigation since Gribkowsky was convicted.
Having appeared at Gribkowsky's trial, Ecclestone told the Munich state court he felt pressured into paying the cash because he was worried the banker would make unfounded allegations about his tax affairs to Her Majesty's Revenue & Customs.
"I paid because he threatened to go to the Inland Revenue," Ecclestone said at the time.
Gribkowsky, who was on the board the Bayern Landesbank, was accused with Ecclestone of conspiring to undervalue F1 when its rights were sold in 2006, so that Mr Ecclestone would retain control of the sport.
If found guilty, Ecclestone could face a jail term which would bring down his Formula One empire.
Ecclestone's rise began in the late 1970s when he bought Formula One's television and marketing rights and has built it up into one of the world's most profitable sporting events on the planet.