The afternoon ceremony was held at Canongate Kirk, followed by a reception at nearby Holyroodhouse, Queen Elizabeth's official residence in Edinburgh, The Daily Telegraph reported.
The wedding was a modest affair compared with the recent ceremony in Westminster Abbey for Prince William and the former Kate Middleton. While Phillips, who plans to keep her maiden name, is the queen's oldest granddaughter and 13th in line to the throne, she has no royal title.
But hundreds of people waited to catch a glimpse of the couple, the royal family and Tindall's fellow rugby stars, with about 30 camping out overnight. Prince William and his wife, the duchess of Cambridge, got the biggest cheer as they arrived.
Phillips, wearing a floor-length short-sleeved ivory dress and a short veil, was escorted into the church by her father, Mark Phillips, Anne's first husband.
The ceremony was the first royal wedding to be held in Scotland since Anne married Timothy Laurence, now a vice admiral in the Royal Navy, in 1992 at Crathie Kirk near Balmoral. The couple were married in Scotland because the Church of England refuses to marry divorced people.