Valverde wins the sprint from the front, denying Bardet, Woods and Dumoulin in attritional race that fractured on leg-breaking final climb.
The Spanish team fell short of its goals to place at least one rider on the podium, although it won two stages and the team prize.
Alejandro Valverde and Nairo Quintana were second and third in the Vuelta entering Tuesday's time trial.
With its two key climbers only seconds out of the overall lead, Movistar is looking like the team to beat at the Vuelta.
With what may be his final shot at a world title looming, Alejandro Valverde must decide how deep he wants to go at the Vuelta a España
Movistar did not land either of its three GC riders onto the Tour de France podium, so it will try the same tactic at the Vuelta a Espana.