Nibali crossed the finish line as second rider behind teammate and first leader of the Spanish grand tour, Janez Brajkovic, earning the Italian 22 seconds of breathing space on the next best of his GC rivals, Sergio Henao and Rigoberto Uran from Sky. Alejandro Valverde (Movistar) is a further seven seconds in arrears with Roman Kreuziger (Saxo-Tinkoff) at 32 seconds and Joaquim Rodriguez (Katusha) nearly a minute off the pace.
"I don't know if I'm the favorite, but I'm happy to have taken some time from my rivals," Nibali told AS.
"Tomorrow is the first stage with a summit finish. The goal is to stay among the overall leaders."
The 28-year-old, who is also attempting to claim the Giro d'Italia, Vuelta double this season, preferred instead to shift the focus to the efforts of his Astana teammates following their victory.
"The team have been fantastic. It was a great time trial," he said, clearly happy. "We have remained united and have been strong from beginning to end. Jani [Brajkovic] has had very bad luck recently so it's fair to let the red jersey.
"I'm in very good condition. The Vuelta is a very hard and long race. There are very important stages to come so we have to go day-by-day."