The fire service said that the four occupants of the vehicle managed to get out unhurt and the fire has been contained.
Traffic is being diverted to the IP4 main road.
The fire occurred in the south tunnel and the north tunnel was closed as it was being used as an emergency evacuation route. This tunnel on the road from Vila Real to Amarante is expected to reopen shortly.
A bus fire on 11 June closed the tunnel for a week.
The twin road tunnel was opened to traffic in May last year and is the longest in Portugal at 5,665 metres.