The piece of art - titled 'Ladylike' - was originally expected to fetch between £50,000 and £85,000, but failed to make the price bracket.
'Ladylike', which included smatterings of the late singer's blood, was sold alongside many other pieces of Doherty's art, diaries, guitars and other possessions.
A total of 17 items were available, all of which sold. Most of the lots were sold online, while a jacket was bought for £1,000.
The auction followed a 10-day exhibition of the musician's work, titled 'On Blood: A Portrait of the Artist'.
A spokeswoman for the gallery told NME: "We had so much interest from fans during the exhibition. At the time of we weren't selling any of those things. But people really wanted to be able to purchase them. So we thought we'd do an auction and make it open to the public rather than price it."
On the Winehouse painting, she added: "The 'Ladylike' painting was never intended to be sold through the exhibition. It was never intended for auction. It doesn't actually belong to Peter, it's being sold by a private seller."
Doherty was a close friend of Winehouse, saying at the time of her death last year that he was left "bewildered" by the news.
Last month, he claimed that her father Mitch Winehouse barred him from attending her funeral.