Gilbert, one of the pre-race favorites, lived up to his billing with a time of 4 hours, 41 minutes, 31 seconds in the 118.9-mile dash from Passage du Gois to Mont des Alouettes.
Cadel Evans of Australia crossed the finish line 3 seconds behind Gilbert and 3 seconds ahead of Norwegian Thor Hushovd.
Defending champion Alberto Contador of Spain got caught in traffic after a late crash along the course and finished the day in 82nd place, 1 minute, 20 seconds behind Gilbert.
The race continues Sunday with a 14.2-mile race around the town of Les Essarts. The Tour culminates July 24.