Authorities say the pursuit began following a carjacking in Perris just after 9:30 a.m.
The chase reached speeds up to 100 miles per hour at times, and passed through Murrieta and Temecula before crossing into San Diego County.
The pursuit ended when three Customs officers at the border station opened fire and shot and killed the suspect after he began moving forward through the crossing.
"The CHP terminated their pursuit of the vehicle which continued to the border where the vehicle stopped, then started to back up before going forward again," San Diego Police Lt. Lee Norton said. "At that point, Customs officers felt threatened and they fired on the vehicle striking and killing the male driver."
It remains unclear whether the man was armed. He has yet to be identified but police say the suspect was alone.
No officers were injured.
The crossing was shut down to southbound vehicle and pedestrian traffic following the incident.
CNS contributed to this report.