The race took place in the western coastal town of Sables d'Olonne, in the Loire region.
Voeckler was the best performing Frenchman in this year's Tour de France, finishing fourth and wearing the coveted yellow jersey for ten days.
He almost didn't compete at all after his sponsor pulled out. His determined efforts and modest style won him many new fans and reignited interest in the annual race which dates back to 1903.
In the 380-metre race on Wednesday, in which the jockey sat in a two-wheeled cart behind the horse, as is common in French horse racing, he was pitted against a horse called Othello Bourbon ridden by the jockey Eric Raffin.
8,000 people were there to watch the event and Voeckler got ahead of the horse on the first lap. However, his cycle power was no match for horse power as the thoroughbred moved ahead to win the race.
Races pitting horses against cyclists are common in France, and it is rare for horses to be beaten.