Although police did not release the name of the painting, French media said it was worth around $10 million.
Police said there had been no sign of a break-in at the apartment located close to the Elysee presidential palace and that the owner, a woman, was away when the painting disappeared. She is in the process of divorcing, the prosecutor's office added.
Basquiat, an American artist of Haitian-Puerto Rican descent, died in 1988 at age 27. In 2013 his painting Dustheads fetched a record $48.8 million at an auction in New York.
A movie on his life, Basquiat, was released in 1996 to critical acclaim.