Alain Lipietz, a Greens European Parliament deputy, and his sister Helene had sued SNCF for transporting their father and three relatives to a wartime transit camp that sent Jews off to Nazi concentration camps.
The French state could not have been unaware that transportation to the Drancy transit camp near Paris was a "prelude to deportation" to concentration camps, an SNCF lawyer, Yves Baudelot, quoted the judges as saying on Tuesday.
SNCF and the French state were ordered to pay around $77,000 to the plaintiffs, Baudelot told Reuters.
The court also said SNCF had never objected or protested against conducting the transportations, and had put Jews in freight carriages without food or minimal standard of hygiene, Baudelot quoted the court as saying.
Baudelot said his client would appeal against the verdict. "I'm amazed by the ruling. I can't understand it," he said.
He said the railway could not be held responsible for the transportation because it had been forced to co-operate with German occupying forces during the war.
"SNCF had no liberty of manoeuvre. The [Nazis] told SNCF by letter that they had to do everything the German authorities wanted, and if someone refused, they would be shot," he said.
Alain and Helene Lipietz had told the court their father, Georges, had been sent by train in mid-1944 from Toulouse to the Drancy transit camp, usually the last stop for French Jews before they were put on trains to death camps.
He was freed from Drancy on August 18, only days before Paris was liberated by Allied forces. The plaintiffs said SNCF billed the state for that transport, which came two months after Allied forces had landed in Normandy.
A similar suit in 2003 failed when a Paris court ruled that it could not establish that SNCF was responsible for transporting Jews.
Of the 330,000 Jews living in France in 1940, 75,721 were deported to death camps and only about 2,500 returned.