The "Dangerous Liaisons" actor sued the paper and two of its journalists over the February 2015 story, part of the so-called SwissLeaks investigation into a tax evasion scheme run by HSBC. Le Monde had claimed Malkovich had stashed money in a Swiss account to avoid paying tax.
The court fined the two journalists behind the story 1,500 euros ($1,700) each and the newspaper's director of publications 1,000 euros. The three were ordered to pay the actor 10,000 euros between them.
The ruling also instructed the paper to publish a statement summarising the ruling on both its front page and the home page of its website.
"My clients will obviously be appealing," said their lawyer Christophe Bigot.
Malkovich's lawyers welcomed the ruling. Malkovich, 62, was one of several celebrities listed by Le Monde among the "elite tax evaders" to have had a secret Swiss account between 2005 and 2007 -- a claim Malkovich has rejected.
"Not only did John Malkovich not defraud tax authorities" he "never had an account with HSBC", Julia Minkowski, one of his lawyers, told the court in July.
The only Swiss account he ever had was a securities portfolio with a bank later bought by HSBC, Minkowski added, accusing the journalists of dragging the actor's name through the mud to sell a poorly-researched story.
She said the actor had declared his securities account to US tax authorities before closing it on November 30, 1999, a month before the creation of HSBC's Swiss private banking arm.
The SwissLeaks investigation was a collaboration by a several leading international newspapers into tax evasion by the rich and famous.