Rafferty can be seen playing the vintage white Fender Esquire in the 1988 video for the song Shipyard Town.
The guitar, made in 1954 and said to have previously belonged to ex-Beatle George Harrison, was sold at Bonhams in London, alongside three other guitars and several awards put up for sale by the Paisley-born star's daughter Martha.
The Paisley-born star's guitar went to an anonymous European buyer for £10,000 after a bidding war in the auction room and online.
Some eight lots raised a total of £26,287.50.
Rafferty, who died in 2011 aged 63, started out in folk group The Humblebums with Billy Connolly and formed Stealers Wheel with Joe Egan in 1972.
His most famous hit, Baker Street, reached No 3 in the UK and No 2 in the US in 1978. It is best known for its iconic saxophone solo.