The unidentified suspect was shot twice when he reached for something inside his vehicle at West Union Street and Del Rosa Boulevard, deputies said.
Deputies first pulled over the driver at Sixth Street and Del Rosa after receiving calls about a man with a gun. The suspect's vehicle matched a witness's description.
When deputies got out of their patrol car, the suspect fired several shots through the back window of his vehicle, shattering the glass but not hitting deputies, sheriff's Sgt. Ed Gonzales said.
The man drove off but pulled over at West Union and Del Rosa, where deputies fired on him when they suspected he was reaching for a weapon, deputies said.
The man's condition was unavailable. Deputies said they recovered the man's firearm.