The race drama in Stage 20 was about who would join Nibali on the podium after a largely ceremonial ride on Sunday to the Champs-Elysees in Paris.
TOUR de FRANCE: Winners list | Images from bicycle racing’s greatest event
It will be Frenchmen: Jean-Christophe Peraud in second and Thibaut Pinot in third. Their times were enough to bump Alejandro Valverde of Spain out of the running for the top three.
Only 15 seconds separated the three men as the stage began.
The result marks the first French podium finishes since Richard Virenque in 1997.
Martin, the world time trial champion, clobbered the field over the 54-kilometer (34-mile) ride from Bergerac to Perigueux.
