Investigators say the deputy was serving a restraining order at a home near Dawn and Buckeye Roads on Friday night when the suspect started shooting at him.
The deputy was able to return fire, hitting the man at least once, before the suspect took off.
The sheriff's office had been searching for the shooter for hours and called for all residents to shelter in place.
The suspect has been identified as Douglas Popke of Mariposa.
He is now in custody and receiving treatment at the hospital.