The incident occurred on the 32500 block of Crete Road around 10 a.m.
The male victim was shot in the hand and treated for lacerations to his head at a local hospital. The suspect fled the scene in the victim's car.
"Deputies located a suspect and the car in the San Clemente area," said Orange County Sheriff's Department Lt. Jeff Hallock. "A short pursuit took place which ended in the San Onofre area."
The search for the suspect in the San Onofre area was terminated just before 6 p.m., with the gunman still at large, according to the OCSD.
What sparked the shooting remains unknown. No further details were released.
Deputies said they were following new leads.
CNS contributed to this report.