Wiggins maintained his advantage of 30 seconds over Australian Rohan Dennis by finishing safely in the peloton in the 76.1 mile (122.4 kilometer) eighth stage, with American Lawson Craddock third at 1 minute, 48 seconds.
The 2012 Tour de France and Olympic time trial champion posted a total time of 28:22:05 to add the most prestigious American race to his resume.
He took the general classification lead in the second stage, a time trial on Monday, and was never seriously challenged.
"It's right up there," Wiggins told the NBC Sports Network, when asked how highly he rated his victory.
"It's always an honor to win the yellow jersey. I set my stool out to win the Tour of California and I've done that now. At 34, it's nice to still be winning at this age."
Wiggins also vowed that if he rides in the Tour de France in July, it will be in support of Sky teammate Chris Froome, the defending champion.
"Chris wants to win a second tour and I think everyone's behind that, including myself, and he's defending champion and he's earned the right to do that.
"(If) I am fortunate enough to be at the tour it will be in support of Chris. I continue to stand by that."
Cavendish had to work hard to edge German John Degenkolb by a few centimeters in the sprint finish, with Slovakia's Peter Sagan, the winner of Saturday's seventh stage, in third place.
"I'm in the form of my life," said Cavendish.
1 Mark Cavendish (GBr) Omega Pharma - Quick-Step Cycling Team 2:53:50
2 John Degenkolb (Ger) Team Giant-Shimano
3 Peter Sagan (Svk) Cannondale
4 Matthew Harley Goss (Aus) Orica Greenedge
5 Danny Van Poppel (Ned) Trek Factory Racing
6 Thor Hushovd (Nor) BMC Racing Team
7 Lars Boom (Ned) Belkin Pro Cycling Team
8 Zakkari Dempster (Aus) Team NetApp - Endura
9 Alex Howes (USA) Garmin Sharp
10 Kiel Reijnen (USA) UnitedHealthcare Professional Cycling Team
1 Bradley Wiggins (GBr) Team Sky 28:22:05
2 Rohan Dennis (Aus) Garmin Sharp 0:00:30
3 Lawson Craddock (USA) Team Giant-Shimano 0:01:48
4 Tiago Machado (Por) Team NetApp-Endura 0:02:02
5 Adam Yates (GBr) Orica GreenEdge 0:02:14
6 Peter Stetina (USA) BMC Racing Team 0:02:30
7 Johan Esteban Chaves Rubio (Col) Orica GreenEdge 0:02:39
8 Laurens Ten Dam (Ned) Belkin Pro Cycling Team 0:03:01
9 Javier Alexis Acevedo Colle (Col) Garmin Sharp 0:03:05
10 David De La Cruz Melgarejo (Spa) Team NetApp-Endura 0:03:06
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