Police said the driver and his passenger had joined the A94 motorway at the Altötting junction, east of Munich, going in the wrong direction.
After driving for about two kilometres, it collided with a car coming the other way, carrying four people, around 5 am.
Both the driver and passenger in the car going the wrong way died, along with three people in the other car.
The badly injured survivor was rushed to hospital, a police spokesman said.
The autobahn was closed in both directions for several hours but has since been reopened.