Two branches of the group's operations and several of its leaders in France have been fined.
The case came after complaints from two women, one of whom said she was manipulated into paying more than 20,000 euros (£18,100) 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.
Ban 'still possible'
Unlike the US, France has always refused to recognise 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 organisation itself has been charged, she says.
Tommy Davis, spokesman for the Church of Scientology International, told BBC News that the court had acted "in total violation of the European Convention on Human Rights and French constitutional guarantees on freedom".
The case "fell flat on its face", he said.
"The fines will get thrown out on appeal. We've had similar cases before and in other countries. If it has to go to the court of human rights we're confident we will win there."
Speaking by phone from the US, he said it was a "political gesture" against the organisation, but "Scientology will continue to grow in France".
The Church of Scientology was founded in 1954 by the late science fiction writer L Ron Hubbard, and includes Hollywood stars such as John Travolta and Tom Cruise.
In the case leading up to Tuesday's ruling, a woman said she was sold expensive life-improvement courses, vitamins and other products after taking a personality test.
A second woman alleges she was fired by her Scientologist boss after refusing to undergo testing and sign up to courses.
The organisation denied that any mental manipulation took place.
The court was unable to impose a ban because of a legal amendment that was passed just before the trial began, preventing the banning of an organisation convicted of fraud.
However, that amendment has now been changed.
"It is very regrettable that the law quietly changed before the trial," Georges Fenech, the head of the Inter-ministerial Unit to Monitor and Fight Cults, told French TV.
"The system has now been put in place by parliament and it is certain that in the future, if new offences are committed, a ban could eventually be pronounced," he said.
A lawyer defending Scientology's operations in France said there would be an appeal.
Eric Roux, a spokesman for the Celebrity Centre, urged France to recognise Scientology's "legality".
"Religious freedom is in danger in this country," he said.
France has always refused to recognise 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.
Quoted for truth. It'll be interesting to see what happens at the appeal.