Valverde won the mass sprint ahead of Jarlinson Pantano (Trek-Segafredo) and Arthur Vichot (FDJ) and claim his third stage win in the week of racing.
Valverde had launched a late attack alongside Dan Martin (Quick-Step Floors) 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.
"At that final lap, I knew Martin would be jumping away at that point next to the Stadium because he had done so in the past," Valverde said.
"I just went after him, though it took a lot for me to close the gap, when he stopped I could see that our advantage was decent. Since it wasn't the best cooperation between us two, we ended up starting that downhill sprint at a very much slower speed than the pursuit group. I just barely managed to win the stage.
Tour de France champion Chris Froome (Sky) tried to salvage some pride with a late attack on the final lap but could not maintain the effort. He finished 30th in the overall standings.
Valverde, who also won the Volta a Catalunya in 2009, the same year he won the Vuelta a Espana, 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.
"To be honest, I wasn't expecting to get these results," Valverde said. "I knew I was in good condition leading up to this race, and those final training rides with Rojas and my team-mates in Andorra the week prior did good on me, but you had to keep in mind that I had spent a whole month without racing, since the Vuelta a Andalucia, while some other rivals like Alberto had a better racing pace.
"My plan was to go day-by-day, without setting my sights on the bigger goals, but my legs got better and better through the race, even more so today. The Volta is a race that I really like, and every time I take the start here is with an aim to do things well."