The Tinkoff-Saxo cyclist defended the lead he established on the opening day during the race's sixth and final stage, an individual time trial in which he finished second behind winner Tony Martin.
After going a year without a multistage race title, Contador has now won the Tour of Basque Country and last month's Tirreno-Adriatico, along with runner-up finishes at the Tour of Algarve and the Volta a Catalunya.
The five-time Grand Tour winner previously had won this race in northern Spain in 2008 and 2009. He took control of this edition, the 54th, during the first stage when he broke away from Alejandro Valverde on an uphill climb.
"Of course when you win, it boosts your confidence but you still have to keep working," Contador said. "It couldn't have gone better for me at the start of this season. I hope to be 100 per cent for the Tour (de France)."
Michal Kwiatkowski of Poland finished the race in second place, 49 seconds behind Contador. Jean-Christophe Peraud of France completed the podium, 1:04 behind Contador.
Valverde entered the day in second place at only 12 seconds behind Contador, but the Movistar cyclist fell to fifth in the final standings, 1:07 back.
Martin, the three-time world time trial champion, won the 26-kilometre (16-mile) leg around Markina in 38 minutes, 33 seconds to claim his second stage win of this year's race after also winning the second leg.
"It feels good," said the Omega Pharma-Quick Step rider. "I lost some (time trials) before this and my morale was down. So to come in here and win a stage and the (time trial) is really good for me and for my team."