The ceremony took place five years after officials refused to register the church's London chapel as a place of marriage, the Guardian reported Sunday.
The couple, Alessandro Calcioli and Louisa Hodkin, both 25, sued to have their religious rights recognized and in December, the supreme court sided with them. Justices ruled the chapel was a "place of meeting for religious worship" and overturned a 1970 ruling that religious worship involved a supreme being.
Calcioli and Hodkin described their marriage as a historic victory against "inequality and unfairness."
"It has been a long, five-year battle to achieve a simple freedom -- the right to marry in our own church with a service in accordance with the rites and customs of our religion and surrounded by our friends and family," they said. "All weddings should be magical and momentous for the couple concerned, but we are conscious that ours, as the first for our religion in England, has its own place in history."
A church spokesman described the wedding as a "historic day for religious equality and freedom for all in the U.K.," saying the newlyweds had "paved the way" for other Scientology couples.
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