Valverde took the first of four stages on the simple 6km course starting and finishing in San Fernando by two seconds from Simon Spilak (Katusha) with Tyler Farrar (Garmin-Sharp) and Jurgen Van Den Broeck (Lotto Belisol) four seconds off the pace.
Katusha's Maxim Belkov laid down a competitive time early on which was only bettered by the top four, Patrick Gretsch (Argos - Shimano, +6s) and Stef Clement (Blanco, +9s).
Bart De Clercq (Lotto Belisol) and Martijn Keizer (Vacansoleil) matched Belkov's time, which was 10 seconds off the eventual winner's pace of 6:46 - set as the last rider out.
Red jersey Valverde's victory last year came soon after his return from a doping ban.
The race also known as the Ruta del Sol continues on Monday with a 164km run from San Fernando to Ubrique.