The Virgin train struck the small hatchback at the crossing in Cleghorn, South Lanarkshire shortly before 7pm on Saturday, but the occupants of the vehicle were able to get out before the impact.
It was dragged 80 yards under the train, which was bound for Glasgow and had 77 passengers on board.
British Transport Police (BTP) are investigating the incident but “driver error” is currently thought to have been the cause.
Speaking last night Inspector Brian McAleese said officers were called to the scene and worked to ensure the safety of those on the train.
He said: “It’s miraculous, there were 77 passengers on the train and three people in the vehicle so it’s a miracle no one was injured in this circumstance and the train wasn’t derailed.
“Anyone that does use a crossing on a regular basis should pay cognisance to the signage and doesn’t take their time when they’re on the railway infrastructure.”
He added: “Had it been a bigger vehicle this could have been far worse.”
The Peugeot 107 was left wedged under the train after it was hit at 100mph, Insp McAleese said.
Following the crash, engineers managed to remove the car from underneath the train using cutters after a number of hours.
The train, which suffered minor damage in the crash, was taken back to Glasgow around 11pm with the passengers still on board.
In 2014, it was reported that the Cleghorn level crossing was the second most dangerous in Scotland.
The ABC Railway Guide lists the crossing as having a “high” risk rating for vehicles.
The publication says it had 25 incidents of misuse in the year leading up to September 2014, and a further six were recorded afterwards.
Cleghorn sees more than 200 passenger and freight trains use the crossing each day, at speeds of around 100mph.
BTP said earlier: “Fortunately, all occupants of the vehicle were able to exit before it was struck by train. There are no reported injuries at this stage.”
The BTP also added: “Our priority is to ensure the safety of everyone on board the train and the vehicles occupants and look to understand how the car came to be on the tracks.”