The journalist, Igal Sarna, was ordered to pay the couple $32,500 (Â£25,000) by a court in Tel Aviv.
Judge Azaria Alkalai said that the allegations had not been substantiated by witnesses.
The couple had vigorously denied the story.
Mr Sarna wrote on Facebook two years ago that Sara Netanyahu had stopped her husband's convoy on a highway one night during a row and ejected her husband.
He said he had heard the account from several people, including a member of the prime minister's security detail, and that he had attempted to verify their stories.
He declined to name his sources, telling the court that they were refusing to testify because they were "afraid".
Mr Sarna works for Yediot Aharonot newspaper which is often critical of Mr Netanyahu.
In March, at the opening of the case, Mr Netanyahu told the court that the journalist's post was a "lie".
"Anyone who knows anything about motorcade security knows that something like that cannot happen," he said.
Mrs Netanyahu said that although she had had arguments with her husband over the years, she could not remember one taking place in a motorcade.
The Netanyahus had sought 280,000 shekels ($79,300; Â£62,200) in damages.
The court awarded Mr Netanyahu 60,000 shekels in damages and Mrs Netanyahu 40,000 shekels. The couple were awarded 15,000 shekels costs.
Israeli Prime Minister Benjamin Netanyahu and his wife, Sara, have won a libel case against a journalist who claimed Mrs Netanyahu had once thrown her husband out of a car in a convoy.