Enrique Ayon, 24, is facing two counts of attempted murder and other charges with a possible penalty of 63 years to life. He pleaded not guilty.
Bail was set at $2 million.
Ayon was captured Tuesday in Lake View Terrace in L.A. County after an alert driver recognized his license plate number from a freeway message sign.
The charges resulted from gunfire incidents along Interstate 805 north of the San Ysidro border crossing in which a 26-year-old man was shot in the leg and later on Interstate 5 where an ambulance was struck.
Shots also were fired at a police officer assisting a motorist. No one was injured in those incidents.
The Associated Press contributed to this report.