Christie's auction house did not immediately identify the absentee buyer who agreed to pay USD 965,000 for the sunburst-finish guitar yesterday.
Dylan's legendary performance at the festival in Rhode Island 48 years ago marked his rupture with the folk movement's old guard and solidified his shift away from acoustic music, like "Blowin' in the Wind," to electric rock 'n' roll, such as "Like a Rolling Stone."
But Dylan's "going electric changed the structure of folk music," said Newport Folk Festival founder George Wein, 88.
"The minute Dylan went electric, all these young people said, 'Bobby's going electric. We're going electric, too.'"
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Christie's had expected the guitar, which was sold with its original black leather strap and Fender hard shell case, to go for far less: USD 300,000 to USD 500,000.
The previous record for a guitar sold at auction was held by Eric Clapton's Fender, nicknamed "Blackie," which sold at Christie's for USD 959,500 in 2004.
The pilot's daughter, Dawn Peterson of Morris County, N.J., said that her father asked Dylan's management what to do with the instrument, but nobody ever got back to him.
Last year, she took it to the PBS show "History Detectives" to have it authenticated, and rock-memorabilia experts matched its telltale wood grain to close-up color photos of Dylan's instrument taken during the 1965 festival.
Dylan's attorney and his publicist didn't respond to email and phone requests for comment. Dylan and Peterson, who declined to be interviewed, recently settled a legal dispute over the items. The terms weren't disclosed.
By going electric, Dylan helped lead a movement that gave rock 'n' roll lyrics the density and ambiguity of literature.
Exactly what happened at the festival on July 25, 1965, has become enshrouded in legend, and to this day, the debate persists over whether those who booed were angry over Dylan's electric turn or were upset over the sound quality or the brief set.