My son was in a car accident, hit by another driver. My son received a DUI for BAL of .09. Will the other driver be at fault or my son?

Yes, your son appropriately received the DUI.  In terms of who is at fault, the fact he was drunk driving doesn't help.  When did it happen? Day or night? How did it happen? Did someone run a light or stop sign? Did someone speed? Did someone try to avoid the accident and the car hit your son's car or vice versa due to your son's drunken driving? 
Did each report it to the insurance companies? What was the outcome there? Has anyone been sued and has it reached a courtroom or mediation yet? What did the police report say?

Bottomline, it may be one person's fault or both parties' faults.  In California, if your son sued, his damages would be reduced by his percentage of fault. 

Do you have a criminal defense lawyer? Is this your son's first DUI? First crime? Try www.attorneypages.com, then check his or her disciplinary record at attorney search at www.calbar.ca.gov.