The unanimous verdict Friday upheld lower court refusals to exempt the Drummondville, Que., family's child from the controversial multi-denominational course.
In the verdict, Justice Marie Deschamps wrote the parents did not prove their religious rights were infringed or that the school board's refusal to exempt their child violated their constitutional rights.
"Parents are free to pass their personal beliefs on to their children if they so wish. However, the early exposure of children to realities that differ from those in their immediate family environment is a fact of life in society," she wrote.
"The suggestion that exposing children to a variety of religious facts in itself infringes their religious freedom or that of their parents amounts to a rejection of the multicultural reality of Canadian society and ignores the Quebec government's obligations with regard to public education."
The case centred on a couple from a central Quebec town who wanted to have their child removed from the course, which the Quebec government introduced in 2008.
They claimed the class violated their freedom of religion by forcing their children to be exposed to religious beliefs that were different from the family's.
Speaking at a news conference, the mother, who can only be identified by her initials, S.L., said she was disappointed with the ruling and believes the consequences could be serious.
She said they'll stay vigilant in the hope that another legal challenge might be mounted. She and her supporters say the course trivializes faith by treating students to a religious buffet.
"My son is in fourth grade and he already asks questions about his own religion and I find it sad that it's happening at such a young age," S.L. said.
"There's a time for everything and I think that teaching about other religions should be done a little later, when the kids are a little older."
The family filed a suit against the schoolboard and the Quebec government, but failed to convince a Quebec Superior Court justice to grant the exemptions. The province's Court of Appeal refused to hear the case.
Quebec introduced the ethics and religious culture curriculum to replace the former Protestant and Catholic religious courses for all students except those in Grade 9.
The government billed the course as a way of fostering harmonious relations among students of different backgrounds, and of introducing them to religious practices and traditions from around the world as well as from Quebec.
Mark Phillips, S.L.'s s lawyer, says he believed that the ruling left the door open to a future challenge against the course. He says his clients were hampered by the fact there was little time to prepare evidence as the course was still in its infancy.
"They lost because, according to the rules of evidence, they are the ones who have the burden," Phillips said.
"But one should be very careful to avoid concluding that today's judgment in any way validates the constitutionality of the program."
Two of the nine judges agreed with the majority decision but expressed reservations about the class. Justice Louis LeBel, joined by Justice Morris Fish, said that the only evidence prepared was a textbook and some expert reports about the course itself.
"The evidence concerning the teaching methods and content and the spirit in which the program is taught has remained sketchy," LeBel wrote, adding that it made it hard to see any impact on the students.
"As a result of the state of the record, however, I am also unable to conclude that the program and its implementation could not, in the future, possibly infringe the rights granted to the appellants and persons in the same situation."
The Quebec government applauded the decision.
In an interview with The Canadian Press, Education Minister Line Beauchamp said the high court saw the course as a vehicle for co-existence and tolerance, rather than for an indoctrination of kids.
When the course was first launched, the Education Department dealt with more than 1,600 requests for exemptions. For 2011-12, that number was only 50.
Quebec has about one million students attending primary and secondary school.
Phillips said he's not discounting that some future family might successfully win the legal battle. He said there is a myth about the course that it is completely neutral.
"It's cultivating a certain non-religious worldview which trivializes (all) religions and presents them in a way which discourages students from adopting religious beliefs and practices," Phillips said.
"Quebecers need to remain vigilant because it's not excluded that a future challenge could be successful.''
(With files from Martin Ouellet in Quebec City)