Sagan, a two-times world road race champion, clinched the relatively flat 192.5km stage into Morro Bay, but his Bora-Hansgrohe teammate Rafal Majka retained the yellow jersey he won on Monday's hilly ride through Northern California.
Majka leads Lotto NL-Jumbo's George Bennett with Team Sky's Ian Boswell third in the overall standings.
Daniel Jaramillo of UnitedHealthcare Pro Cycling is leading the King of the Mountain competition.
Monday's stage included a violent crash by Latvian rider Toms Skujins, who suffered a concussion, a broken collarbone and grazing that forced him to withdraw from the race.
The seven-day race continues on Wednesday with a 159.5-km ride from Santa Barbara to Santa Clarita.
