The Deceuninck-Quick Step sprinter mastered the rising finish to beat Jasper Philipsen (UAE-Team Emirates) and Peter Sagan (BORA-hansgrohe) on a stage where the peloton preferred to take in the stunning California scenery than ride at a pace expected of the WorldTour.
“I had strong legs today, but also a formidable lead-out, which kept me out of the wind, protected me in those hectic final kilometres and delivered me where I needed to be for the sprint," Jakobsen said.
"This uphill drag to the line forced me to push hard, but I was confident and waited for the perfect moment to kick out and take another win for our team."
Jakobsen's fast finish to a slow-motion stage aside, race leader Tegan van Garderen (EF Education First) had a calamitous final 10km of the 212.5km stage from Laguna Seca to Morro Bay.
Van Garderen crashed after snapping a chain, remounted on team-mate Lachlan Morton's bike, took a wrong turn and was then slowed by another crash.
Confusion reigned at the finish as it appeared the American had lost his overall lead but the race jury reinstated van Garderen to the top position with the remainder of the classification board also essentially unchanged.
Gianni Moscon (INEOS) remains in second place at six seconds and Stage 2 winner Kaspar Asgreen (Deceuninck-Quick Step) third at seven.
More to come.