The California Highway Patrol says the driver drove around the downed railroad crossings on East Conejo near Peach Avenue.
An Amtrak train then collided with the car, launching it about 200 feet up the tracks.
The driver, later identifed as 48-year-old Danny Shelton, died at the scene.
His passenger rushed to a local hospital, where officals said she later died.
Investigators have not yet identiified the woman.
None of the 1,300 passengers on the train were hurt.
The CHP is investigating the crash.