Carmakers have long feared that Mr. Trump might retaliate, either with tariffs or trade restrictions, if they didn’t support his effort to dismantle the rules, which were designed to fight climate change. After California struck its deal with the four automakers, the administration and Justice Department pushed a series of unusual legal and policy moves against the state and those companies — including an antitrust investigation — that were widely perceived as retaliatory.

Representatives from General Motors and Fiat Chrysler declined to comment on the record, since the legal case is still unfolding. In a statement, Toyota said that it had “entered into this legal action not as a plaintiff or a defendant, and not to favor any political party. Toyota is intervening to impact how emissions standards are applied.”

On Wednesday Mr. Trump wrote on Twitter, “Thank you” to General Motors, Toyota, Fiat Chrysler and the other automakers, “for standing with us for Better, Cheaper, Safer Cars for Americans. California has treated the Auto Industry very poorly for many years, harming Workers and Consumers. We are fixing this problem!”

The split among the auto giants is far more consequential than simply the pursuit of divergent legal strategies among corporate competitors. “This is a huge rift. These vehicle manufacturers are splitting up in unique ways,” said Barry Rabe, a professor of public and environmental policy at the University of Michigan. “Imagine an administration unleashed in a second term to confront any industry that does not do the political bidding of the president,” he said.

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It was that calculus that concerned many automakers at a gathering earlier this month in the sleek Washington office of the Alliance of Automobile Manufacturers, the industry’s powerful lobbying arm. The companies were split over whether to back Mr. Trump’s revocation of the right of California and other states to set strict state rules on climate-warming tailpipe pollution.