While his Kazakh team took victory on stage one, Slovenian Janez Brajkovic became the individual race leader.
Already the Giro d'Italia winner in May, Nibali flashed across the finish line in the coastal resort of Sanxenxo in second place behind Brajkovic but still triumphantly punched the air.
Luxembourg outfit RadioShack Leopard were second on the wind-blasted time trial course in the remote northwesterly region of Galicia, 10 seconds back, while Belgians Omega Pharma-Quick Step were third at 16 seconds.
Two likely contenders lost time on Nibali and Astana with Spain's Alejandro Valverde, the 2009 Vuelta winner, and his Movistar squad finishing 29 seconds back in fifth spot and Joaquim Rodriguez 59 seconds adrift.
"I'll be wearing the leader's jersey tomorrow but Vincenzo is the number one favourite, our one and only team leader, and hopefully I'll pass it on to him soon," Brajkovic told reporters.
"Then hopefully he'll stay in the lead all the way to Madrid."
Briefly the leader of the Vuelta in 2006, Brajkovic said he had low pre-race expectations of returning to the top spot.
"For the first time this year, though, I felt good," added the Slovenian, the 2010 Criterium du Dauphine winner who crashed out of the 2013 Tour de France. "I was in pain but it was the kind of pain you like to feel.
"Getting the lead is like a dream. I was not expecting to win it, there are so many other strong squads here."
Rodriguez, third in the 2012 Vuelta, said his 12th-placed Katusha team suffered badly on the twisting 27.4-km course where strong winds buffeted the riders.
"We got off to a bad start," he explained. "We lost a lot of riders early on and got split up and that really affected our performance in the last part where we should have gone quicker."
Brajkovic will wear the leader's jersey on Sunday's stage from Pontevedra to the Alto do Monte da Groba summit finish, a little-known 11-km climb never previously tackled in the Vuelta.
The race ends on September 15.
(Editing by Tony Jimenez)
