Awarded by the French animal protection group 30 Millions d'Amis (30 Million Friends), the offbeat animal-themed prize traditionally wraps up France's book award season, and is bestowed in the Paris restaurant which hosts the real Goncourt each year.
This year's winner, "Domestic Carnivores" by Erwann Creac'h, is about a vet who answers emergency home calls for pets, only to find himself face-to-face with the distress of their often lonely, bewildered masters.
Creac'h, 38, who works in Paris but is originally from western Brittany, said he was "very surprised" by the honour, and that he simply sought to "share with others what I see and learn every day on my rounds."
"We don't often talk about solitude in our society, or about the profound relationship that exists between man and animal," he said.
"People come in and want to talk about their animals' problems but they end up talking about their own -- and that's what I wanted to share."
The award carries €1,000 ($1,338) in prize money, which the winner donates to the animal charity of his choice.
Houellebecq, who won the Goncourt last year for his work "The Map and the Territory", was asked to sit on the jury because of his well-documented passion for animals -- which he has called a "crazy love."
For years the controversial writer was spotted with his pet terrier at his side, up until the dog's death in March this year.
"There are lots of things that I have made fun of in my literary career, but this relationship with a pet, especially for a person who is alone, is something I would never mock," Houellebecq said.
But the writer did say he would have gone for a different title. Instead of "Domestic Carnivores", he suggested "The Only Person Who Ever Loved Me."