Nibali took advantage of his effectiveness against the clock to overtake veteran American, Chris Horner, Xinhua reported.
Nibali finished fourth overall on the stage, behind Cancellara, who is favourite to win the time trial in the forthcoming World Championships.
Cancellara rode the 38.8 kilometre stage, which included a small climb, in a time of 51 minutes.
Tony Martin, another specialist against the clock, followed him while Domenico Pozzovivo was third.
Horner, the overall leader going into the stage, finished twentieth on the day, 2.54 minutes slower than Cancellara.
He slips to joint third overall, 46 seconds behind Nibali and 13 behind Nicolas Roche.
--IANS (Posted on 05-09-2013)