For reasons not immediately known, the motorbike travelled in the wrong lane before colliding with the car driven ion the opposite direction, 3.5 kilometres from the Göschenen exit, police said in a news release.
The motorcyclist succumbed to injuries at the site of the collision, the release said.
One of the occupants of the car was transported to a local hospital for observation, police said.
Both vehicles, bearing German licence plates, were write-offs.
The Alpine tunnel, linking the cantons of Uri and Ticino in southern Switzerland, was closed from 11.30am to 2pm, police said.
This resulted in tailbacks as long as eight kilometres from its entrances, the Touring Club Schweiy said on its website.
A highway passing through the Gottharrd Pass, which provides an alternate route, remains closed as usual at this time of the year because of snow.
The tunnel accident came a day after another deadly collision caused by a wrong-way driver, this time in a three-car pileup on the A1 motorway between Rorschach in the canton of Saint Gallen and Arbon in the canton of Thurgau.
A 71-year-old motorist died and three people were injured after his car was hit by another car, driven by a 58-year-old man, which was travelling in the wrong direction, Saint Gallen police said.
The vehicle of the older driver, a German man living in the region, flipped and ended up in a field, while a third car was also damaged, police said.
The motorist’s wife and a passenger were treated for minor injuries and given psychological counselling, police said.
Passengers in the other vehicle also escaped serious injury, while rescue workers had to extricate the trapped driver, a Swiss resident from Bosnia-Herzegovina, from the car, police said.
All three vehicles were damaged beyond repair, while a section of the A1 motorway was closed for four hours.
An accident involving a vehicle towing a caravan that left a passenger slightly injured, meanwhile, led to tailbacks outside the San Bernardino tunnel in the canton of Graubünden after it was closed for two and a half hours on Saturday.