The Slovak Tinkoff rider bided his time before winning a sprint finish at the famed Laguna Seca motorsport circuit in Monterey, his second triumph of the 2016 race after a victory in Sunday's first stage.
The 2015 world champion had effectively given up hope of retaining his Tour of California crown after a disastrous third stage which left him with no chance of challenging in the general classification.
But Sagan took consolation with victory in Wednesday's fourth stage, a 134.8 mile (217 kilometer) run from Morro Bay up California's scenic Pacific Coast Highway before its climax at Laguna Seca.
The 26-year-old took the line honors with a time of 5hrs 16min 33sec, ahead of Belgium's Greg van Avermaet (BMC Racing) and Australia's Nathan Haas (Dimension Data).
France's Julian Alaphilippe of the Etixx-Quick Step team strengthened his grip on the yellow jersey after finishing in 10th place.
Alaphilippe leads the general classification with an aggregate time of 18:06:17, 22 seconds clear of American rider Peter Stetina of the Trek-Segafredo team.
Lotto's George Bennett remains in third place overall.
Stage five on Thursday sees the peloton start in the rolling hills of northern California's wine country before winding its way to Lake Tahoe in the Sierra Nevada Mountains.