The ruling comes a year after Europe's top rights court said France had interfered with the religious freedom of the Christian sect when it imposed a tax on donations from followers.
France must reimburse 4.59 million euros ($5.7 million) for the taxes "unduly paid," the court said in a statement, as well as €55,000 ($68,000) in costs and expenses.
The Strasbourg-based court, however, rejected a Jehovah's Witness demand for €250,000 in damages -- one euro for each of the sect's followers in France -- as well as another request for France to scrap altogether its efforts to collect taxes from the group.
The Association of Jehovah's Witnesses claimed the French government was trying to repress their activities by imposing in 1998 a tax assessment that amounted in total to €45 million ($56 million), covering the period from 1993 to 1996, though France seized only a fraction of that amount.
Philippe Goni, a Jehovah's Witnesses lawyer, welcomed the ruling he said recognised the sect had been subject to "genuine discrimination" by French authorities.
"It's a fresh victory for Jehovah's Witnesses, who have been denigrated and stigmatised since 1995," he said, referring to a parliamentary report into French sects, which followers said aimed to marginalise the group.