The California Highway Patrol said the agent, whose name was not released, was airlifted to a hospital Monday afternoon for treatment of non life-threatening injuries.
CHP Officer Scott Beauchene said the injuries were not serious, but the Riverside-based agent was airlifted because of the remote location of the attack on Interstate 10 near the Highway 111 exit.
Border Patrol spokesman Aaron Van Zee said two people were arrested after an extensive search. The third assailant remained at large.
Authorities have not named the suspects or said what prompted the traffic stop and led up to the fight.