Wearing the leader's yellow shirt for the final leg, the Spaniard peddled into Paris in the middle of the pack, which was good enough to finish 23 seconds ahead of Cadel Evans of Australia. American Levi Leipheimer was 31 seconds back in third place.
The final leg was won by Italian Daniele Bennati.
Contador, who races for the Discovery Channel Team, won a crown tarnished by recent doping-related expulsions, including Denmark's Michael Rasmussen, who led the overall standings before being removed from the race by his team Wednesday.
It was the third notable doping-related dismissal in the world's premier cycling competition. Kazakhstan's Alexandre Vinokourov and his Astana team left Tuesday and the Cofidis team withdrew Wednesday. Last year's event also came under scrutiny after American Floyd Landis' victory was clouded by doping suspicions.