Nibali, the defending Tour de France champion, had a difficult week, being distanced by the major riders in Sunday's stage as the Italian struggles to find his form.
Quintana beat second-placed Bauke Mollema of the Netherlands by 18 seconds with Colombian Rigoberto Uran taking third place, 31 seconds off the pace, according to provisional results after Tuesday's final time-trial won by Swiss Fabian Cancellara.
Cancellara looked in ominous form five days before the Milan-San Remo classic, the first of the five classic one-day races of the season.
Frenchman Pinot, third overall in the 2014 Tour de France, finished fourth overall ahead of Spain's Contador. They were 35 and 39 seconds off the pace respectively.
Another Tour de France favourite, Briton Chris Froome, pulled out before the race due to illness.
(Reporting by Julien Pretot; Editing by Ed Osmond)
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