The crash happened on Buena Vista Drive near Paseo Verde at about 7 pm.
Both the deputy and the other driver, who was driving under the influence of alcohol, sustained very minor injuries.
CHP officers say 61-year-old Bryan Berlier either didn't stop at the stop sign right at the intersection or failed to yield, crashing with the deputy's vehicle.
The deputy was taken to hospital as a precaution. Photos show his patrol car was severely hit, and the entire front side was crushed.
Berlier was arrested and booked into the Merced County Jail.