Louisa Hodkin and her fiancé Alessandro Calcioli tied the knot at London Church Chapel on Sunday.
The couple, who are both 25 and from East Grinstead, had to take legal action last year after the registrar general of births, deaths and marriages refused to register the church for the solemnisation of marriages.
But a supreme court judge overturned a high court ruling in December that stated the services were not “acts of worship”, paving the the way for the marriage to take place.
“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.
A Church of Scientology spokesman added: “We are delighted that Louisa and Alessandro can now be married in their church in front of their family and fellow parishioners.
“They have paved the way for other Scientologist couples.”