Prince William and wife Kate, who tied the knot in April in a public display of royal pomp and pageantry, and the British monarch herself were among the guests in the Canongate Kirk, where the Queen worships when staying in Edinburgh.
A few hundred fans waving Union Jack flags lined the street leading up to the church as guests sporting hats and kilts arrived for Britain's second royal wedding of the year.
After the ceremony, traditional Scottish bagpipe music was played as the newlyweds, the bride wearing an ivory floor-length dress and a full-length veil, emerged from the church to loud cheers from the crowd outside.
Phillips, 30, was considered something of a "royal rebel" when she was younger, having her tongue pierced as a teenager.
But the daughter of Princess Anne and her first husband Mark Phillips has followed in her mother's footsteps to enjoy a successful horse-riding career.
In 2006 she won an individual gold on her horse Toytown at the World Equestrian Games in Germany, helped Britain win a team silver and was voted BBC sports personality of the year.
Well-known rugby player Tindall, 32, was part of the England team that beat Australia to win the World Cup in 2003. The couple met during that tournament.
Their wedding was due to be followed by a reception at the Palace of Holyroodhouse, the Queen's official residence in Scotland.
Several thousand fans gathered outside the church and the palace hoping to catch a glimpse of royalty, police estimated.
However, the low-key festivities took many in Edinburgh by surprise. "Who's getting married?" asked Alberto Alvarez, 38, who has come from Spain for a holiday.
"I am very happy for them anyway," he added.
(Writing by Olesya Dmitracova; Editing by Mark Heinrich)
