The service was conducted by the Reverend Sheila Munro, minister for the parishes of Inverkeithing and North Queensferry.
The pair wed at Mr Brown's home in North Queensferry, in Fife, in a ceremony conducted by a Church of Scotland minister. Mr Brown's brother John acted as best man.
Afterwards, the couple kissed in the garden in front of a battery of television cameras and press photographers.
They said in a statement: "We are overjoyed. It has been a wonderful day and a lovely ceremony."
The surprise wedding at 1015BST took place in front of more than 30 friends and members of the couple's families.
The service was conducted by the Reverend Sheila Munro, minister for the parishes of Inverkeithing and North Queensferry.
The newly-weds are holding a small reception for family and friends before setting off on honeymoon in Cape Cod, Massachussets, the area which is home to America's first political family, the Kennedys.
The wedding announcement was delivered in a surprise statement on Wednesday evening from Mr Brown's special adviser, ending speculation over when the couple would tie the knot.
'Commitment' to constituency
Speaking before the ceremony, Rev Munro said their decison to wed in Fife showed Mr Brown's commitment to his constituency.
"I think it will be very special for them to show that he is part of the community. He is not travelling to London to get married.
"I feel I am giving something to them, involving God in their special day and they will be involving God in the rest of their lives."
Prime Minister Tony Blair and his wife Cherie did not attend, but were among the first to offer their congratulations.
A spokeswoman for the Blairs said they were "very happy for the chancellor and Sarah Macaulay".
The couple plan to hold a party for friends and colleagues when they return from honeymoon in September.
Secret engagement
They will move into Mr Brown's central London apartment, and split their time between there and his home in Fife.
It emerged that Mr Brown, 49, had proposed to Miss Macaulay in January and a date for the wedding was set soon afterwards.
Mr Brown and Ms Macaulay, 40, met six years ago when her PR firm, Hobsbawn and Macaulay Communications, was involved in arranging Labour Party events. They began dating in 1996.
Despite widespread speculation about their relationship, there was no hint that wedding plans were being drawn up before Wednesday's surprise statement.
It emerged that the announcement of the impending wedding had been displayed in the normal way in the parish where the ceremony would take place.
As the couple posed for photographs, a neighbour said: "We've been waiting for it for a long time.
"It's a great day for the village. We're all delighted for them."
Mr Brown has had several serious relationships over the years, but it has been suggested that his passion for politics has previously hindered his personal life.