Yates, who rides for Mitchelton-Scott, attacked in the last kilometre of a hilly stage, which had included four categorised climbs, and Movistar’s Valverde was unable to close the gap in time.
Astana’s Spanish rider Ion Izagirre, who finished fourth, holds a seven-second advantage over world champion Valverde heading into the final day of the event.
“It feels good,” Yates said. “I’ve had a really good off-season. I’ve been really consistent with my training and doing everything correctly and it just goes to show – when you commit like that, everything comes together.”