The court ordered the carrier to pay 46,000 euros to the man and 100,000 euros to the health insurer that has been covering his costs after he said he was poisoned with drain cleaner on the Bordeaux to Paris flight.
Marc-Fredaine Niazaire was taken ill during the flight and hospitalised on landing. He was operated on for a problem with his oesophagus and sued Air France for poisoning him with a "seriously toxic liquid" used to clear drains.
A criminal enquiry concluded in 2010 that there was nothing to prosecute, after which Niazaire launched a civil case seeking 680,000 euros in damages.
"The symptoms arose at the same time as Mr Niazaire ingested a coffee and biscuit. They appeared suddenly," the court ruling said, adding that Niazaire had never previously been treated for stomach problems.
An Air France spokeswoman said the company would study the ruling and decide on whether to appeal.
Niazaire's lawyer, Didier Parr, said he was "very happy."
"The coffee cost Air France 146,000 euros. That's an expensive coffee," he said.
But he said he was disappointed by the amount of compensation, saying his client had had to undergo numerous operations, including for the reconstruction of his oesophagus.
Air France lawyer Maylis Casati-Ollier said during court hearings in November that the company had no responsibility in the case.
"Mr Niazaire drank the same water as everybody else, but he was the only person on board to get sick," she said.