The Slovakian took the top spot on the podium by a full 15 seconds ahead of LottoNL-Jumbo’s Jos van Emden on the 10.6km stage, with Etixx-Quick-Step’s Julian Alaphilippe continuing his remarkable run of form with a third place.
Sagan’s win moves him to the top of the overall classification, 28 seconds up on former leader Toms Skujins; Alaphilippe sits in third place, 45 seconds behind Sagan.
Sergio Henao was Team Sky’s leading rider on the stage, crossing the line with the seventh best time, moving him up to fifth place, with the Colombian needing to make up 55 seconds on Sagan on Saturday’s mountain stage to have a chance at the win.
Twenty-year-old Brit Tao Geoghegan Hart claimed the 17th best time in Big Bear, leaving him in fourth place in the Young Rider classification.
Tour of California, stage six: Big Bear (10.6km)
1. Peter Sagan (Svk) Tinkoff-Saxo, 12:31
2. Jos van Emden (Ned) LottoNL-Jumbo, at 15s
3. Julian Alaphillipe (Fra) Etixx-Quick-Step, at 19s
4. Joey Rosskopf (USA) BMC, at 20s
5. Daniele Bennati (Ita) Tinkoff-Saxo, at 22s
6. Tom Zirbel (USA) Optum P, at 26s
7. Sergio Henao (Col) Team Sky, st
8. Jay McCarthy (Aus) Tinkoff-Saxo, at 27s
9. Robert Gesink (Ned) LottoNL-Jumbo, st
10. Daniel Oss (Ita) BMC, at 28s
1. Peter Sagan (Svk) Tinkoff-Saxo, 22:15:23
2. Toms Skujins (Lat) Hincapie Racing, at 28s
3. Julian Alaphillipe (Fra) Etixx-Quick-Step, at 45s
4. Joey Rosskopf (USA) BMC, at 49s
5. Sergio Henao (Col) Team Sky, at 55s
6. Jay McCarthy (Aus) Tinkoff-Saxo, at 56s
7. Robert Gesink (Ned) LottoNL-Jumbo, st
8. Ben King (USA) Cannondale-Garmin, at 58s
9. Dion Smith (Nzl) Hincapie Racing, at 1:03
10. Haimar Zubeldia (Esp) Trek Factory Racing, at 1:04