It was among more than 100 guitars put up for sale by the star to raise money for a substance abuse centre he has set up on the Caribbean island of Antigua.
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The identity of the person who bought the 1956 sunburst Fender Stratocaster is not known. The telephone bidder requested anonymity.
In total, the auction at Christie's in Manhattan raised more than £3.1m, many times the pre-sale estimate.
The Grammy award-winning rocker was not present to see his property go under the hammer. However, in a statement just after the auction, he said: "I can't believe it. I am totally overwhelmed. I had no idea the auction would do so well."
Versace guitar strap
Christie's itself seemed stunned by the bidding. Most of the instruments went for three or four times their estimated prices. Even guitar straps, albeit ones designed for Clapton by Versace, fetched fabulous amounts. One, with an estimated value of £500 to £750, sold for almost £900.
"It's fantastic. It's one of the world's great events," said Richard Chapman, curator of the collection and author of "The Complete Guitarist".
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Over 1,000 people attended the auction in person, with over 60 phones set aside for telephone bids. The actor Michael J. Fox bought two of the guitars through an intermediary.
"Eric Clapton means a lot to me," he said in a statement after the auction.
Clapton had earlier said he was planning to buy one of his guitars back, but Christies said the rock star made no bids for any of the guitars.
Clapton's Crossroads Centre in Antigua was founded in 1997. It charges almost nothing to treat residents of Antigua, and asks about $9,000 a month for others.
Other items sold included a 1954 Fender Stratocaster which sold for £132,000; a 1974 Martin 000-28 for £108,000; a rare 1958 Gibson Explorer with a solid body design for £83,000; and a red 1991 Gibson Firebird - which was given to Clapton by a fan - for £24,300.
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Official Yardbirds site
Christie's
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