That is nearly double the price of his previous most expensive work, which was bought a year ago.
The untitled work was done in oil-stick, acrylic and spray paint and depicts a skull.
It went to a telephone buyer from Japan, following 10 minutes of bidding with a client in Sotheby's.
Cheers and applause erupted in the room when the work was sold.
Basquiat, a native New Yorker, died in 1988 of a heroin overdose aged 27. He had been an artist for just seven years.
Once a graffiti rebel from Brooklyn who sold drawings for $50, he is now in the same league as Pablo Picasso and Francis Bacon, she says - part of a rare group of artists whose work has sold for more than $100m at auction.