Officers received a 911 call from a woman in the Walmart parking lot on Olive Avenue and Loughborough Drive, who said the shots came from another vehicle shortly after 2 am.
The woman told authorities that the suspect's vehicle, a black Chevrolet Tahoe, had followed them along Highway 99.
Emergency crews treated the victim and then airlifted him to a Modesto hospital in critical condition.
Authorities believe the shooting took place in Merced or Atwater, and that the suspect drove away from the scene.
The CHP said the suspect is considered armed and dangerous.
Anyone with information is asked to call Investigator Vince Villegas at 209-356-6631.