The custom-made Fender Rosewood Telecaster was also used by the late musician during the filming of the Beatles documentary film "Let it Be," which chronicled the often-prickly production of the album of the same name.
Musician Delaney Bramlett sold the instrument. He received it as a gift from Harrison in 1969.
The guitar originally went on sale in London in 1999 but failed to meet the asking price of $318,000 and was withdrawn.
"He (Harrison) played it on January 30, 1969, on the rooftop of Apple Records in London, the last time the Beatles performed together in public," said auction house president Bill Miller.
Harrison died in 2001 after a long battle with cancer.