The 34-year-old made the piece of work, drawn in lipstick, while she was dating Pete Doherty.
It was expected to fetch between £30,000 and £40,000.
The portrait is marked with Kate's own lip prints and has troubled rocker Doherty's blood stains on the canvas.
Pete's message reads: "Who needs blood when you've got lipstick?"
The work initially failed to sell but was then shifted privately following the auction.
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