Sagan won in the 177.5km stage from Palmdale to Santa Clarita by about half a bike length from Michael Matthews (Orica-Greenedge) and Tyler Farrar (Garmin-Sharp), the Cannondale man living up to the tag of favourite for the day.
The Slovakian had appeared to be in the wrong position for the race to the line, but a dart to the right of the field changed his fortunes.
"With about 700 metres, I was in about 10th position," said Sagan, who collected his ninth Tour of California stage in four years.
"It was a bit crazy, there was confusion because all the teams were trying to get up there. I got to the right to the front with about 100 metres left."
Acevedo (Jamis), who had triumphed in a gruelling summit finish in high temperatures the previous day, managed to retain his 12-second lead in the general classification from Tejay van Garderen (BMC), with Ireland's Philip Deignan (United Healthcare) a further 15 seconds back.
"I was very tired after yesterday," said Acevedo. "I never felt very good the whole day today, so I just tried to stay in there. Fortunately, the teams were all working to together for a sprint finish, so the day wasn't difficult."
There had been an early attempt at a breakaway, with Andy Schleck (RadioShack Leopard) and Lieuwe Westra (Vacansoleil-DCM) among four riders with a five-minute lead midway through the stage, but they were reeled in with 13km remaining.
Stage four is expected to produce another sprint finish, despite a couple of small climbs on the road between Santa Clarita and Santa Barbara.