The potraits, painted by Bacon in 1975 and 1980, had never been on display to the public and resurfaced in a private collection earlier this year after descendants of the original collector decided to sell.
Self-Portrait and Three Studies for Self-Portrait sold for 15.3 million pound and 14.7 million pound respectively, Daily Express reported.
"We reached new heights at Sotheby's with the highest total we've ever achieved for contemporary art in London," said Alex Branczik, Sotheby's head of contemporary art.
Self-Portrait was painted at the height of Bacon's career, in the period which followed the suicide of his former lover George Dyer in 1971.
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The triptych Three Studies for Self-Portrait shows the artist, who was then in his 70s and becoming increasingly haunted by the inevitability of death, with his eyes downcast.
"These magnificent works narrate the latter half of a most extraordinary decade for Francis Bacon," said the auction house.
Born in 1909, Francis Bacon was known for his bold, emotionally charged and raw imagery. The Irish-born English figurative painter died on 28 April 1992.