The 2009 Vuelta winner nipped ahead of world champion Sagan on the final corner of the 195-km flat ride from Linares to Almaden in stage nine to top the points category and gain 10 bonus seconds on Frenchman Molard, who finished 30th in the stage in a packed 52-man peloton and retained the red jersey.
Valverde's Movistar and general classification rivals Sky decided to bide their time for most of the stage which was led by an Iberian trio of Tiago Machado, Jorge Cubero and Hector Saez until they were caught by the peloton with six km to go.
Valverde, 38, also took victory on the second stage of this Vuelta and finished third, one place behind Slovakian Sagan, in Friday's stage.
Sunday's stage nine is a 200.8-km mountain route from Talavera de la Reina to La Covatilla with a summit finish, with the riders taking their first of two rest days on Monday.
(Reporting by Richard Martin; editing by Clare Fallon)
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