Spaniard Valverde, 36, pipped Colombian Jarlinson Pantano at the finish line to claim his third stage win in a week.
Valverde had launched a late attack alongside Irishman Daniel Martin with three kilometres to go of the 138.7km race around Barcelona, which culminated with laps of Montjuic, the site of the 1992 Olympic Games village.
Valverde's fellow Spaniard and Movistar team mate Marc Soler came third overall, 1:16 adrift.
Tour de France champion Chris Froome tried to salvage some pride after his poor display on the sixth stage with a late attack on the final lap but could not keep up the pace and was soon pegged back. He finished 30th in the overall standings.
Valverde, who also won the Tour of Catalonia in 2009, the same year he won the Tour of Spain, had triumphed in La Molina on stage three and in the fifth stage in Lo Port.
He took a commanding lead over Contador into the final stage after coming second on Saturday, and showed resilience to bounce back after being docked a minute due to illegal pushing by his Movistar team mates in Tuesday's team time trial.
"Today I felt good after a really hard stage yesterday, everything was easier today because of the team," Valverde told reporters.
"I knew Daniel (Martin) would attack when he did as he always does that and I worked very hard to stay with him and in the end I won by a hair's breadth."
(Reporting by Richard Martin; Editing by Toby Davis)
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