Cruise's publicist Arnold Robinson confirmed to The Associated Press that the ceremony had taken place, and later said in a statement that it was performed by a Scientology minister before more than 150 relatives and friends.
Holmes wore a fitted Giorgio Armani off-the-shoulder bridal gown with a train in ivory silk cadis adorned in Valenciennes lace and Swarovski beaded crystal embroidery, and Cruise also wore a handmade, Armani tuxedo.
Holmes' father Martin Holmes, walked her down the aisle, and she carried a bouquet of flowers made by Armani. It included calla lilies wrapped in leaves of galax and steelgrass.
Cruise's best friend, David Miscavige, was best man, and the matron of honor was Holmes' sister, Nancy Blaylock.
In his statement, Robinson said Cruise and Holmes "officialized their marriage" in Los Angeles before coming to Italy. He did not immediately reply to an e-mailed question about whether that meant they had been married in a civil ceremony.
Outside, fans and residents hoped for a glimpse of the celebrity couple, as oil-fed torches glowed from the battlements of the Odescalchi castle, which towers over the town on the shores of Lake Bracciano. Tiny candles, placed in the castle's windows, flickered romantically as the couple and fellow stars gathered in the town about 25 miles northwest of the Italian capital.
The castle's imposing battlements supposedly hold the ghost of Isabella de Medici whose husband strangled her in 1576 because she took lovers. Legend also has it that Odescalchi Castle weddings may be cursed - several celebrity marriages held here in recent years ended in divorce, reports CBS News correspondent Allen Pizzey.
Following the ceremony, Cruise and Holmes were serenaded at the reception with a special performance by Italian singer Andrea Bocelli.
Guests were treated to Italian hors d'oeuvres followed by a multi-course meal. Cruise and Holmes cut a five-tiered white chocolate wedding cake decorated with marzipan roses and studded with white chocolate chips.
Earlier, Holmes wore a black dress and boots before she changed into a Giorgio Armani gown for the wedding. Cruise came from Rome, where the family had been staying in a luxury hotel near the Spanish Steps, in a van and, sporting dark shades, waved to fans.
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to read about the dress.
When the groom drove up, Holmes, anxiously gesturing with a hand, watched from a castle window.
Other VIPs arriving in limousines or vans through the castle gates included Brooke Shields, Richard Gere, Jennifer Lopez and Jim Carrey.
Pouring rain had forced Holmes and her baby to take shelter under large, green umbrellas as they left their limousine. But the sun was shining on the castle when Cruise arrived.
As the sun began to set, candles were placed in pots along the road to the castle. Men wearing tuxedos and women holding up the hems of their long gowns walked up the steep path to the castle.
Police patrolled the castle's walls and all vehicles were banned from Bracciano's center.
"When I first walked here, I didn't know why they chose this place," said Emily Roeder, 19, of Atchison, Kansas, who came to Bracciano for the day from Florence, where she is studying. "Then I saw the castle and the streets all around, and it's really romantic."
Hundreds of the town's 14,000 residents and fans of the stars braved intermittent rain to catch a glimpse of the arrivals.
"I want to see at least one of them - even if it's not Tom Cruise," 15-year-old Erica Bandiera said.
The first guest to drive through the castle's gates was Roberta Armani, niece of the fashion designer.
Holmes was giving Cruise a wedding gift of a Vacheron Constantin watch engraved simply, "I Love You," the watch company said in a statement. It said she bought the gift in Los Angeles last week.
Scientology ceremonies contain many elements of traditional weddings, including rings and vows. But they also include certain Scientology fundamentals, including vowing never to go to bed without communicating about any differences.
A spokesman for the Church of Scientology for Rome, Fabrizio D'Agostino, said an exchange of vows with a Scientology rite was not legally recognized in Italy, and would have to be preceded or followed by a civil union.
Bracciano Mayor Patrizia Riccioni said her office had not received a request to celebrate a civil wedding as of midday Friday.