Houellebecq, who came close to winning the Goncourt in 1998 and 2005, has divided readers and critics with edgy, sex-fuelled satires that have drawn accusations of obscenity and racial provocation.
He is the best-known French writer abroad, and his stories often feature tales of modern male angst with novels such as such as Atomised and Platform, both translated into English.
As it is each year, the prize was announced at the chic Drouant restaurant in Paris by the Goncourt panel of literary bigwigs who voted seven to two in favour of Houellebecq.
La carte et le territoire, one of four finalists, satirises the Paris art world, in the tale of Jed Martin, an artist who gains global fame by photographing old Michelin maps.
The book has garnered enthusiastic reviews, with Liberation newspaper calling it a "masterpiece".
Sales have stayed buoyant despite a row last month over accusations of plagiarism, which the author has dismissed as "ridiculous".
One of the four finalists, Virginie Despentes's Apocalypse bébé (Apocalypse baby), a mix of social satire and lesbian romance, was awarded the Renaudot prize, a kind of unofficial complement to the Goncourt, usually announced at the same time.