The painting titled "Untitled", also set a record price for an American artist at auction.
The subject of much of Basquiat's work - ordeals endured by blacks in America - is finding renewed resonance in the wake of nationwide U.S. protests since 2014 about the shootings of unarmed black men by police.
Sotheby's had valued the work at more than $60 million and guaranteed the seller an undisclosed minimum price regardless of the bidding at the auction.
"Breaking $100 million for a work which is that recent is definitely extraordinary". For reference, the last time the Basquiat painting was sold was in 1984.
Japanese billionaire Yosaku Maezawa bought "Untitled" at Sotheby's auction house on Thursday night.
Last year, he became the highest-grossing American artist at auction, generating US$171.5 million from 80 works, according to Artprice, and his auction high has increased at least tenfold in the last 15 years.More news: Trump says he's 'very close' to naming a new FBI director
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"I am happy to announce that I just won this masterpiece". Eventually, Maezawa will house the work-which was nearly never seen between its initial purchase in 1984 and now-in a museum he is building in Chiba, Japan, according to Sotheby's. "I hope it brings as much joy to others as it does to me, and that this masterpiece by the 21-year-old Basquiat inspires our future generations".
"I've never seen so much emotions in such a painting", he said.
"Now he goes into the pantheon of great, great artists", said Oliver Barker, chairman of Sotheby's Europe. "We are thrilled that it was purchased by Yusaku Maezawa for his planned museum so others will have a chance to experience its magic firsthand", Billault said.
Sotheby's concludes its week of sales on Friday.
A little background on the mysterious Maezawa: The 41-year old entrepreneur began his career in the music industry in the 1990s when he founded Start Today Co., an import business which sold CDs and vinyl.
Gregoire Billaut is the auction company's head of modern art. His "The Women of Algiers (Version 0)" fetched $179.4 million at Christie's in NY in 2015. In the space of very few years had gone from from selling drawings for $50 to selling out his first solo exhibition at New York's Annina Nosei gallery, earning $250,000.