Ecclestone did, however, step down Thursday as a member of the board of directors pending the outcome of the trial.
Earlier Thursday, the Munich state court decided to send the 83-year-old Ecclestone to trial following his indictment last May. He faces charges of bribery and incitement to breach of trust connected with a $45 million payment to a German banker, Gerhard Gribkowsky.
Dates for the trial haven't yet been set but proceedings are currently expected to start at the end of April, a court statement said. Bribery convictions can result in prison sentences ranging from three months to 10 years in Germany.
The board of F1's holding company met following the announcement, and Ecclestone reassured it that he is "innocent of the charges and intends to vigorously defend the case," a company statement said.
Although he stepped down from the board, the statement said 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."
Ecclestone's German lawyers, Sven Thomas and Norbert Scharf, said in a statement that "the alleged bribery did not happen."
"The accusations in the indictment based on Gribkowsky's statement are unfounded and do not ... add up to a coherent picture," they added.
Jean Todt, the president of governing body FIA, refused to comment on the German court's decision at an event in Munich on Thursday.
Gribkowsky was convicted in 2012 of taking the payment from Ecclestone in connection with the sale of a stake in F1. He was found guilty of corruption, tax evasion and breach of trust, and sentenced to 8 1/2 years in prison.
Ecclestone acknowledged during Gribkowsky's trial that he made the payment but said he was pressured to do so.
Gribkowsky was in charge of selling German bank BayernLB's 47 per cent stake in F1 to investment group CVC Capital Partners in 2006.
The indictment alleges that Ecclestone and Gribkowsky agreed on the $45 million payment in May that year and sought to cover up its source and recipient; and that the money was paid between July 2006 and December 2007.
Gribkowsky had previously pushed through the payment of a commission of more than $41 million to Ecclestone on the grounds that he "had in his hands the evaluation of the Formula One share and, with that, the sale price," it adds.
In separate legal proceedings in London, German media company Constantin Medien — a former F1 shareholder — is suing Ecclestone and other defendants for up to $144 million, claiming F1 was undervalued by the BayernLB deal.
Ecclestone said in November at the High Court in London that he made a payment to avoid being reported by Gribkowsky to authorities over his tax affairs.
"I made up my mind he needed to be kept quiet," Ecclestone said, asserting that he was "shaken down" by Gribkowsky.
A ruling is expected early this year in that case.
AP Sports Writer Rob Harris in London contributed to this report.