Sagan, riding for Cannondale, jumped to the front just after the final corner to win the 88.7-mile Santa Clarita road race in 3 hours 24 minutes 33 seconds.
"Finally, I got another one," said Sagan, a four-time Tour de France stage winner who claimed his 11th career stage win at the Tour of California and the 66th victory of his career.
"We pulled at the front all day until the finish," he added of his team. "It was an important win for the team and for me."
With his victory secure with about 50 yards left, Sagan, known for his animated victory celebrations, raised his hands off his handlebars and appeared to be playing the piano.
"I was just waving to the fans," Sagan said.
Wiggins, the 2012 Tour de France winner who rides for Sky, finished 15th in the main field to maintain his 30-second lead over Australia's Rohan Dennis of Garmin-Sharp. American Lawson Craddock of Giant-Shimano remained third overall, 1:48 back.
"It was a relatively straightforward stage," said Wiggins, who has held the race lead for a week since winning the stage-2 time trial. "We didn't have to do too much. But it was a pretty fast and tough run-in to the finish. You always have to aware of a breakaway or a crash."
Norway's Thor Hushovd of BMC was second the stage, followed by Dutchman Danny Van Poppel of the Trek team.
There were no changes at the top of the overall standings, with all of the top 10 finishing in the front group.
Luis Romero of Cuba of the Jamis-Hagens Berman squad bolted to the front and raised his arms in victory as he crossed the line. But Romero had only finished two of the 3.1-mile circuits. He was absorbed by the field and eventually finished 18th in the stage.
Garmin-Sharp's Ben King of the United States and Belgian Greg Van Avermaet of BMC entered the final circuits with about a 15-second lead but were caught with about five miles left.
The 720-mile event, which began May 11 in Sacramento, concludes Sunday in Thousand Oaks with a 76.1-mile circuit race. The field will ride three 21-mile circuits each with a 910-foot ascent, followed by three 4.6-mile circuits around Westlake Lake.