The Team Colombia-Highroad sprinter, who was 84th in the General Classification going into the stage, avoided a number of crashes to pip Tom Boonen to the line in Clovis after a 115.4 mile stage which had started in Merced.
After four stages, American Levi Leipheimer leads the race with Cavendish's team mate Michael Rogers second. Lance Armstrong is fourth.
Stage Five is a 134.3 mile race from Visalia to Paso Robles and the race ends on Sunday.