Several trains were delayed, the worst an hour and fifteen minutes on the train that hit the car, which made an illegal turn in front of the train, an Amtrak spokeswoman said.
Oakland police said the driver of the car was not seriously injured and refused medical attention. No other injuries were reported.
The Capitol Corridor train No. 542 struck a car that was crossing the tracks at Embarcadero West and Franklin shortly before 6 p.m., throwing the car off the rails, according to an Amtrak spokeswoman.
As authorities sorted out the crash site, an AC Transit articulated bus attempted to cross at Embarcadero at Broadway, a block north of the accident, but jackknifed and became stuck.
Amtrak spokeswoman Vernae Graham said the incident was still under investigation and didn't know if charges would be filed against either driver.
Such incidents are common on the Embarcadero, which serves as both street and railroad as it passes Jack London Square. The fastest trains can travel along the stretch is 25 mph.
Graham said she sees people and motorists trying to cross the tracks from her office at the corner of Embarcadero and Clay Street.
"I think people underestimate how fast the train is going," she said.