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.
The four novels in the final reckoning for the Goncourt, the oldest and most prestigious in the French-speaking world, dealt in one way or another with the Middle East or the long twilight of France's colonial entanglement in the region.
Winner chosen over lunch
"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.
Although the victor gets only 10 euros ($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.
As well as "Zone", Enard's 2012 story of young Moroccans adrift in Europe "Street of Thieves" has already been translated into English.
But his "Parle-leur de batailles, de rois et d'éléphants" ("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.
The Algerian writer Boualem Sansal was long the odds-on favourite for the prize but failed to make the top four last week with his dystopian vision of a future Islamic caliphate, "2084", its title a nod to George Orwell's classic "1984".
Sansal had the strong backing of Michel Houellebecq, France's most famous literary provocateur, himself a Goncourt winner in 2010, who praised the book's critique of "true Islamic totalitarianism".
With Sansal out, many had thought the smart money was on "Les Preponderants" (roughly translated as "The Principals"), by veteran Franco-Tunisian author Hedi Kaddour.
'Cruel and stupid tyranny'
His novel, set in the Tunisia of the 1920s as resentment at French rule grows, was joint winner last week of the Academie Francaise prize, given by the lofty guardians of the French language known as the "immortals", who rule over grammar and which new words enter their dictionary.
The fact that the Goncourt jury chose to reveal its final four novels in Tunis, where Kaddour, 70, was born, seemed also to indicate they were leaning his way.
Pivot said the highly symbolic announcement in the city's Bardo Museum, where jihadist gunmen killed 21 tourists and a policeman in an attack last March, was to show support for the country's fledgling democracy in the very place "where the most cruel and stupid tyranny had shown its contempt for freedom".
Tobie Nathan's "Ce pays qui te ressemble" ("This country that you resemble") was also said to have its fans on the jury, with its tales of the Jewish Cairo of his childhood and the lost idyll of the city's cosmopolitan tolerance.
The only woman on the shortlist, Nathalie Azoulai, also had a Middle Eastern twist to her pained love story "Titus n'aimait pas Berenice" ("Titus does not love Berenice").
But there was better news for women in the parallel Renaudot prize, won by Delphine de Vigan, who was also the only female writer in contention, for "D'après une histoire vraie" ("From a true story").
Only six women writers have ever won the Goncourt in its 112-year history, including Lydie Salvayre last year for "Pas pleurer" ("Don't cry").