Police and paramedics were called to the Uxbridge Road level crossing in Lakeside yesterday at 1.35pm where a woman and a man were trapped inside their BMW.
Richard Bosman of the City of Cape Town said the two people were in a serious condition after being removed by paramedics and transported to Victoria Hospital.
He said the cause of the crash would be investigated.
No one on the train was injured.
Riana Scott of Metrorail said the accident resulted in delays while police carried out an investigation at scene.
She added technicians were called to the scene and train services on the line were delayed by one hour along the Simon’s Town and Fish Hoek line.
“Both train and vehicle are damaged,” she said.
“Commuters on board the stricken train were assisted while being disembarked from the train involved in the incident.
“Both railway lines [were] closed for the duration of the incident investigation.
“Revised transport arrangements until the police’s on-site investigation [was] concluded and the line is cleared for operation.”
She added that a limited bus service between Retreat and Fish Hoek would be available.