The case came after complaints from two women, one of whom said she was manipulated into paying more than 20,000 euros in the 1990s.
A Scientology spokesman told the BBC the verdict was "all bark and no bite".
France regards Scientology as a sect, not a religion.
Prosecutors had asked for the group's French operations to be dissolved and more heavily fined, but a legal loophole prevented any ban.
Instead, a Paris judge ordered the Church's Celebrity Centre and a bookshop to pay a 600,000-euro fine.
Alain Rosenberg, the group's head in France, was handed a two-year suspended jail sentence and fined 30,000 euros.
Three other leading members of the group were also fined.
Unlike the US, France has always refused to recognize Scientology as a religion, arguing that it is a purely commercial operation designed to make as much money as it can at the expense of often vulnerable victims, the BBC's Emma Jane Kirby reports from Paris.
Over the past 10 years, France has taken several individual members of the group to court on charges of fraud and misleading publicity, but this is the first time the organization itself has been charged, she says.