Movistar rider Valverde, who won the Vuelta in 2009 and is among the favourites for the 70th edition of the race, moved up to fourth overall, 25 seconds behind Colombian Chaves, thanks to his victory on the 209.6-kilometre stretch to Vejer de la Frontera.
Dutchman Tom Dumoulin (Giant-Alpecin) is second overall (+5 seconds), with Irishman Nicolas Roche of Team Sky, who finished fourth behind Valverde's Spanish compatriot Dani Moreno (Katusha) on Tuesday, in third (+12).
Briton Chris Froome, who won a second Tour de France crown at the end of July and is bidding for a rare Tour-Vuelta double, finished safely with the main group and is ninth (+40).
The Sky leader is bunched with some of his main rivals including Colombian Nairo Quintana of Movistar (+36), Spanish pair Joaquim Rodriguez (Katusha, +32) and Valverde and Italian Fabio Aru (Astana, +50).
"Our team set the tempo today like we did on the first road stage," Valverde told reporters.
"Today we stayed calm and we knew it was a long race and we needed to keep some strength in the bank," he added.
"We sat with Katusha who were good but so were we. We sat on and didn’t need to accelerate too hard and then in the last 200 metres I just flew."
Frenchmen Jacques Anquetil (1963) and Bernard Hinault (1978) are the only riders to have won the Tour and the Vuelta in the same year.
(Reporting by Iain Rogers, editing by Pritha Sarkar)
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