A scholar of both Arabic and Persian, Barcelona-based Enard, 43, wove a poetic eulogy to the long history of cultural exchanges between East and West in "Boussole" ("Compass"), and had been the critics' favourite for the award.
The novel has already won the booksellers' prize -- the Nancy-Le Point -- for its nimbly erudite voyage which flies in the face of many of the cliches about the so-called clash of civilisations.
Seven out of 16 critics polled by one of France's leading books weeklies said Enard -- an academic who has lived in Tehran, Berlin and Beirut, where his breakthrough novel "Zone" (2008) is set -- most "deserved" the prize, and he told reporters he was "extraordinarily happy" as the news of his win broke.
"I like a winning book which tells of the world in which we live," the head of the jury, Bernard Pivot, told French radio on the eve of the often-heated lunch at a Paris restaurant over which the winner is chosen.
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Although the victor gets only 10 euros (USD 11) in prize money, the Goncourt almost guarantees a boost in sales of 450,000 copies or more, placing it instantly among the year's bestsellers.
But his "Parle-leur de batailles, de rois et d'elephants" ("Tell them of battles, kings and elephants"), which won the Goncourt's youth prize in 2010, France's second most lucrative literary award, has still to find a English-language publisher.