Louisa Hodkin and Alessandro Calcioli, both 25, married in the historic ceremony in Blackfriars, London, after winning a legal battle at the Supreme Court to exchange vows at the church. It had not previously been legally recognised as a place of "religious worship".
In a statement, the couple said their wedding was a "momentous" day and the culmination of a five-year battle to have their religious claim upheld.
The couple, both from East Grinstead, West Sussex, said: "We are pleased and proud our victory brings to an end inequality and unfairness, not just for Scientologists, but for people of all faiths."
The Supreme Court ruled "religion" should not be confined to faiths involving a "supreme deity".