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The sale was conducted by auction house Phillips in association with Bacs & Russo Game Changers New York Watch Auction.
The Academy Award winner's Rolex GMT Master Reference 1675, the timepiece he wore in Francis Ford Coppola's epic 1979 war film "Apocalypse Now," went for $1.95 million.
Another Rolex worn by golf pro Jack Nicklaus was sold for $1.2 million.
The Rolex GMT Master also features a never-before-seen engraving on the back that reads "M. Brando," which was hand-engraved by Brando himself. It's fitted on a black strap with its bezel — the top ring on the watch that surrounds the crystal — missing. That's because Brando was told to remove the watch while filming because it appeared to look too polished for his character, Col. Walter E. Kurtz, but he kept it on anyway, removing the bezel from its face instead to better suit the role.
The watch would ordinarily be worth between $15,000 and $20,000 on the resale market, Benjamin Clymer, the founder of Hodinkee, a high-end watch publication, told FOX Business.
Clymer says the Rolex GMT Master would be far less valuable on the resale market without its original Bezel, but because of its significance in the movie, it will likely command $1 million or more at the auction.
Brando owned the watch until 1995 when he gave the timepiece to his daughter, Petra Brando Fischer, according to Phillips. A portion of the proceeds will go to charity.
The theme of this year's auction is "Game Changers," dedicated to watches owned by legendary individuals from brands such as Patek Philippe, Piguet, Omega and Breitling.
The Rolex Day-Date Reference 1803 in yellow gold worn by Nicklaus, also known as the Golden Bear, received it as a gift in 1967. Nicklaus won 12 of his 18 professional major championship titles while wearing the 18-karat yellow gold watch, according to Phillips. It was the only watch he's ever worn.
Clymer said the watch would normally fetch around $12,000 on the resale market, but since Nicklaus wore it to win major championships it's become a piece of history and would command at least seven figures.
Proceeds for the sale of Nicklaus' watch will go to his namesake Children’s Health Care Foundation.
The entire Game Changers auction fetched $20.2 million in a White Glove Sale.
FOX Business' Jeanette Settembre contributed to this article.