Fota said in a statement after Wednesday's meeting that the FIA's new stance had "put the future of Formula 1 in jeopardy".
Ecclestone now owns a network of companies which have the exclusive right to sell and market the International Automobile Federation's (FIA) TV rights.
The track at Sonoma will also host the first U.S. FIA World Touring Car Championship, AutoGP World Series and the United States Touring Car Championship in a busy motor sports weekend.
However, Dennis, who first took over as McLaren team principal in 1981, insisted at a news conference that the timing of his departure from F1 was "purely coincidental" and not linked to the team's upcoming FIA hearing.
Whiting's statement contradicted an announcement by the FIA's world council on 24 June which listed the eight Fota teams - McLaren, Ferrari, Renault, BMW, Toyota, Brawn, Red Bull and Toro Rosso - as confirmed entries.
Red Bull's team principal Christian Horner said he respected the FIA's decision.
CNN: Bahrain Grand Prix will go ahead, says F1's ruling body
Neither Symonds or Briatore attended the hearing at the Tribunal de Grande Instance, France's high court, but their representatives argued that procedures adopted during the original investigation were against the FIA's international sporting code.
However, the sport's governing body, the FIA, said it was not surprised by BMW's decision given the difficult global economic climate.
The debate around the eligibility of the appeal centres on article 152 of the FIA's sporting code.
The sport's governing body the FIA said the rule was changed "following a unanimous request from the teams".
The details will be released on Friday after it has been approved by the FIA's World Motor Sport Council.
The case will be heard by governing body the FIA's International Court of Appeal at the organisation's headquarters in Paris.
The teams have two months to come up with alternative suggestions if they do not agree with the FIA's ideas.
BBC: SPORT | Motorsport | Formula One | F1 changes to be revealed
Max Mosley, president of motorsport's governing body the FIA, has repeatedly stressed the need for F1 teams to trim their workforce.
The team will go before the FIA's World Motor Sport Council in Paris on September 21 to hear the findings of the probe.
Maysoon Jayyusi, formerly a Speed Sister herself, now manages the team and is the Palestinian representative on the FIA's Women in Motorsport Commission.
The FIA's world motor sport council has also ratified F1's new 25-18-15-12-10-8-6-4-2-1 points system for the first 10 drivers to finish a grand prix.
However, BBC 5 Live commentator David Croft believes there is a possibility that the teams could stand firm and refuse to back the FIA's proposal.
Motorsport's governing body the FIA issued a revised schedule, with Turkey moving from August to 7 June to allow a summer break for the teams.
F1's governing body the FIA has made the engine proposal as one of three options to cut what it views as the sport's excessive costs.
The qualifying changes are due to go to the FIA's Motorsport World Council on Monday, 24 October and will come into force for the 2006 season if voted through.
Stewart said the Mosley scandal had brought the sport into "disrepute" and "good judgment and taste" personally, or from the FIA's representatives, should have seen him resign.
The FIA's decision to limit the revs of the Seat cars, which had been far faster than the rest of the field, seems to have had some effect.
The other key element is the introduction of a commissioner to represent the FIA at grands prix - a move that is being echoed across all the FIA's championships.
However, Whitmarsh, despite being among the team bosses who want an end to team orders, admitted he was confused by the FIA's decision not to inflict further punishment on Ferrari.
The Tribunal de Grande Instance de Paris ruled last week that the FIA's decision was procedurally incorrect but did not exonerate Briatore or Symonds of conspiring to cause the crash.
He also said the team had been on the brink of being sold to German businessman Oliver Behring as the representative of a group of Arab investors until the FIA's decision.
"We are disappointed by what has happened but in the circumstances we are not going to appeal, " said McLaren team principal Martin Whitmarsh, before the FIA's summary of considerations was released.
Because the FIA's role is mainly focused on financial intelligence, its U.S. counterpart is the Financial Crimes Enforcement Network, not the Securities and Exchange Commission, according to a person who worked on Tuesday's agreement.
That statement had come after Max Mosley, president of F1's governing body the FIA, had reached a compromise deal with Fota chairman and Ferrari president Luca di Montezemolo and F1 commercial boss Bernie Ecclestone.
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