The train struck the car at about 10:30 p.m. Saturday, Dec. 30, near the intersection of East E Street and South Coast Highway 101.
The car was stopped beyond the crossing arms on East E Street, said Deputy Tyler Eikermann of the San Diego County Sheriff's Department.
The train driver attempted to brake, but was unable to stop in time and struck the car, Eikermann said.
Sheriff's deputies had managed to remove the driver of the vehicle before the crash, and then arrested the driver on suspicion of drunken driving, Eikermann said.
There were no reported injuries to train passengers or crew members,said Amtrak spokesman Jason Abrams.
Train service was disrupted for about two-and-a-half hours as a result of the crash, Abrams said.