The auction house said it was very rare for an artist to attend an auction, and it demonstrated the connection Emin felt to the highly personal work.
The price reached for Emin's work, described by the auction house as an iconic piece of 1990s British art, quadrupled her previous sale price record, but Christie's said the market was not overheating.
"There is a very discerning element to this market. It's not a frothy market. People are really making distinct choices. Its a very subjective response to works," Brett Gorvy, Christie's international head of post-war and contemporary art, said after the sale.
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A painting by Peter Doig, the huge oil "Gasthof," sold for 9.9 million pounds, beating the estimated price of 3 million to 5 million pounds, and beating a record set the previous day for one of the Scottish artist's works.
Around 190 bidders from 28 countries took part in the auction, Christie's said, with interest from Europe, North America, the Middle East and Asia.
Bacon's 1967 portrait, one of only two single portrait heads Bacon painted of his friend and rival Freud, was sold by the estate of the British author Roald Dahl for 11.5 million, towards the top range of the auction house's 8 million to 12 million pound estimate.
But the price was a relatively poor showing for a Bacon piece compared with his recent record-breaking at auction. The highest price ever paid for a work of art at auction was the sale by Christie's of a large format triptych in New York last November for just over $142 million. Rival auction house Sotheby's sold a Bacon small-format triptych on Monday for 26.7 million pounds, soaring above a 20 million-pound top price guidance.
Bacon's 14 x 12 inch painting with its distinctive green strokes had been in Dahl's private collection from the beginning. The two were friends and Dahl bought the painting for 2,850 pounds with the proceeds from his children's novel "Charlie and the Chocolate Factory."
Some of the proceeds from the Bacon sale will be diverted to two charities championed by Dahl, and by his family since his death in 1990.
All the buyers from the auction chose to remain anonymous, meaning Emin will have to wait to find out whether her Turner short-listed work will end up in a museum, a wish she expressed the week before.
"My Bed," auctioned for the first time, was sold by the Saatchi Gallery Collection.
Fifteen years ago, the startlingly human elements of the work, which includes discarded condoms and stained sheets, caused a sensation, raising questions about what was and was not art.
The British artist had transformed her bed and the connected detritus from a depressed period in her life into a portrait of sorts, which had been expected to sell for between 800,000 pounds and 1.2 million pounds.
Speaking ahead of the auction, Emin told Reuters TV that the work felt like "a ghost."
"I feel quite sad, and I feel that it's like a fragment of time," she added.