Phinney, riding for BMC, escaped from the front group with 19 miles left and completed the 107.4-mile stage from Pismo Beach to Santa Barbara in 3 hours, 59 minutes, 33 seconds for his seventh career pro win.
Wiggins, the Sky rider who won the 2012 Tour de France, took the race lead after winning the second stage. He finished in the field Thursday to keep a 28-second margin over Australia’s Rohan Dennis of Garmin-Sharp.
Portugal’s Tiago Machado of NetApp-Endura, was third overall — 1:09 back.
Slovakia’s Peter Sagan of Cannondale was second in the stage, and Australia’s Matthew Goss of Orica GreenEdge was third in the same time.