Contador finished third in the 16-mile time trial in Milan, 36 seconds behind stage winner David Millar of Britain, but because of his large lead in the general classification he didn't need to finish first.
Contador, of Saxo Bank-SunGard, ended the three-week grand Italian tour with a total time of 84 hours, 5 minutes and 14 seconds, 6:10 better than Italian Michele Scarponi of Lampre-ISD.
Another Italian, Vincenzo Nibali of Liquigas-Cannondale, grabbed the third spot, 6:56 behind Contador.
Contador -- a three-time Tour de France champion -- took his sixth career Grand Tour title. He won his first Giro since 2008 thanks to his mountain racing, where he was easily the most consistent cyclist despite winning only two stages.
Contador took the lead two weeks ago while climbing Mount Etna and added to it by winning Stage 16, an uphill time trial.