Gaviria's Quick-Step Floors team mate Max Richeze produced an equally nuclear amount of speed in the finale in Elk Grove, which the Colombian capitalised on coming off his wheel.
While Sagan at first followed the pair with Ewan (Mitchelton-Scott) a rear fixture, Gaviria's turn of pace saw the world champion falter, the plucky Aussie beating him to the second step on the podium.
"The other guys from the team did a really good job (to avoid the crash) and also in the final," Gaviria said. "It was really fast and we are happy taking a really nice victory today.
"Max (Richeze) did a really good job because in the last kilometre it was difficult but these guys are really strong and i'm really happy."
Marcel Kittel (Katusha) and Mark Cavendish (Dimension Data) did not contest the final sprint after they were unable to rally from a run of bad luck that befell three of the famous fastmen.
In the space of the final chaotic 12 kilometres, Cavendish suffered a mechanical and waited an aeon for it to be fixed while Kittel and Ewan also took turns by the side of the road. Ewan was barely delayed but the gap for Kittel was just too much.
After his frantic chase back on, Cavendish and his teammates were further delayed by a crash four kilometres from the finish, their day done and dusted.
Five riders spent much of the day out the front on a short leash of around two minutes, the catch made not long before Cavendish's mechanical.
Tejay van Garderen (BMC) remains in the overall lead with a 23 second buffer to Team Sky's Egan Bernal.