The porcelain lavatory was used by the music legend during the three years he lived at Tittenhurst Park, Berkshire, between 1969 and 1972.
Lennon gave it to builder John Hancock, telling him "to use it as a plant pot" after he installed a new toilet.
It was expected to sell for £1,000 but the investor broke the estimate at the 33rd Beatles Convention in Liverpool.
Fab Four expert and auction organiser Stephen Bailey said: "It is unbelievable.
"We had bids coming in from all over the place but it went to a private overseas buyer."
The sale took place in the The Paul McCartney Auditorium at The Liverpool Institute for Performing Arts.
The toilet had been stored in Mr Hancock's shed at home for nearly 40 years, until he died recently.Controversial sleeve
Other items to be auctioned at the sale included one of Lennon's rarest albums.
A mono-sound copy of Two Virgins, which he recorded with Yoko Ono, was sold for £2,500.
The album, which was released in November 1968 was famous for being sold in brown paper bags to cover the controversial sleeve which featured the couple naked.
Another sale item was a small harmonica which had belonged to Lennon's son, Julian, which the musician also gave to Mr Hancock.
Lennon had told the builder that his young son had been driving him mad with it.
The instrument had been estimated to reach £1,000 but sold for £2,500. Its private buyer has indicated it could be loaned out to one of Liverpool's museums.
An unused concert ticket for a Beatles performance in September 1968 on board the Royal Iris ferry sold at the auction for £2,000.