Louisa Hodkin had been refused permission to wed fiance Alessandro Calcioli in a Church of Scientology chapel in central London because it was not legally listed as a place of religious worship.
A High Court judge had ruled in 1970 that Scientology services did not count as acts of worship because they involved no "veneration of God or of a supreme being".
But five judges at Britain's highest court on Wednesday said Hodkin and Calcioli should be able to marry in the Scientology chapel, and that religion should not be confined to faiths involving a "supreme deity".
Hodkin had compared her faith to Buddhism and Jainism -- neither of which feature a deity -- and argued that the 1970 ruling should not be binding because Scientologist beliefs and services had evolved over the past four decades.
Calcioli pronounced himself "ecstatic" after the couple was finally granted permission to marry in the chapel.
"I think the court's definition of religion is excellent. I think it's what most people today would understand 'religion' to be," he said.
Hodkin said the couple hoped to get married in the next few months.
"I am really excited. I'm really glad we are finally being treated equally and can now get married in our church," she said.
But local government minister Brandon Lewis said he was "very concerned" that the ruling will lead to the organisation becoming eligible for tax breaks, and that his ministry was seeking legal advice.
"Hard-pressed taxpayers will wonder why Scientology premises should now be given tax cuts when local firms have to pay their fair share," he said.
Britons can marry in a wide range of religious and non-religious venues, but the location must have official approval.
Scientology, which counts actors Tom Cruise and John Travolta among its supporters, has long been controversial due to allegations of brainwashing and violence, as well as claims that it is designed to trick members out of large sums of money.
In October France's top appeals court upheld a fraud conviction and fines totally hundreds of thousands of euros against the church for taking advantage of vulnerable followers.
Founded in 1954 by US science fiction writer L. Ron Hubbard, Scientology is recognised as a religion in the United States but is treated as a cult in other countries. It claims a worldwide membership of 12 million people.
The church has claimed to have more than 100,000 members in Britain, but only 2,418 Britons listed it as their religion in the 2011 census.