The black sedan was travelling through severe rainfall near Goose Creek, north of Charleston, on Wednesday afternoon when severe gusts of wind threw it up in the air at an intersection.
Footage shows the car being flipped upwards by the strong winds, causing it to spin on its rear wheels before flipping upside down and landing on the roof of another oncoming car.
The Goose Creek Police Department said that the two people inside the car suffered minor injuries and were taken for treatment at a local hospital.
Officials from Berkely County Emergency Management later confirmed that it was a brief tornado during Storm Idalia that had flipped the vehicle.
The close call came as Hurricane Idalia continued to hammer parts of eastern US after making landfall in Florida on Wednesday morning.
Idalia had intensified into a Category 4 hurricane in the early hours of Wednesday, weakening to a powerful Category 3 just before it slammed into the Big Bend region in Florida.
The hurricane struck near Keaton Beach with 120mph winds, ripping down electricity poles and cables across the state and leaving around half a million residents without power.
Widespread flooding affected thousands of homes and swamped the runways at Tampa International Airport while a gas station roof was ripped off by powerful wings in Perry.
At least three people have so far been found dead across Florida and Georgia. Two men were killed in road accidents on Wednesday morning, according to the Florida Highway Patrol.
A third man was killed in Georgia by a falling tree while he was trying to clear another fallen tree off a highway.
Even after the hurricane passed through Florida, Governor Ron DeSantis warned that dangers remain.
He told citizens to not “do anything dumb” and warned looters that they could be shot if they target homes and businesses amid the post-storm recovery.
The storm is now moving through the coastal area of North Carolina throughout Thursday and is expected to move out into the Atlantic later in the day.