The train pushed the car metres along the tracks. Photo / 7 News
A Fire Rescue Victoria spokesman said two crews responded to make the scene as safe as possible.
"The car was towed away and the train was able to be moved to the nearby station where passengers were allowed to exit to the platform," he said.
No one was injured from the collision.
Williamstown and Werribee lines train services between Footscray and Newport stations were suspended for about 90 minutes while emergency services responded.