Phinney enjoyed a 12-second win over runner-up Slovakian Peter Sagan after completing the 173 kilometres from Pismo Beach to Santa Barbara in three hours, 59 minutes and 33 seconds. Australia's Matthew Goss finished third.
With just three days of racing remaining, Wiggins is showing no signs of ceding control.
The 2012 Tour de France champion, Wiggins took his initial lead following stage two and holds a 28-second advantage over Australia's Rohan Dennis.
The tour continues Friday with the 152-km sixth stage from Santa Clarita to Mountain High.
1 Taylor Phinney (USA) BMC Racing Team 3:59:33
2 Peter Sagan (Svk) Cannondale 0:00:12
3 Matthew Harley Goss (Aus) Orica GreenEdge
4 Jasper Stuyven (Bel) Trek Factory Racing
5 Kiel Reijnen (USA) UnitedHealthcare Professional Cycling Team
6 Lawson Craddock (USA) Team Giant-Shimano
7 Thomas Damuseau (Fra) Team Giant-Shimano
8 Greg Van Avermaet (Bel) BMC Racing Team
9 Paul Voss (Ger) Team NetApp-Endura
10 Tiago Machado (Por) Team NetApp-Endura
1 Bradley Wiggins (GBr) Team Sky 17:53:36
2 Rohan Dennis (Aus) Garmin Sharp 0:00:28
3 Tiago Machado (Por) Team NetApp-Endura 0:01:09
4 Lawson Craddock (USA) Team Giant-Shimano 0:01:25
5 Adam Yates (GBr) Orica GreenEdge 0:02:14
6 Peter Stetina (USA) BMC Racing Team 0:02:28
7 Matthew Busche (USA) Trek Factory Racing 0:02:29
8 Carter Jones (USA) Optum p/b Kelly Benefit Strategies 0:02:31
9 Laurens Ten Dam (Ned) Belkin Pro Cycling Team 0:02:33
10 Javier Alexis Acevedo Colle (Col) Garmin Sharp 0:02:34
- Sports & Recreation
- Peter Sagan
- Rohan Dennis
- Bradley Wiggins
- Matthew Goss