Gibernau held his nerve during difficult weather conditions

Gibernau gave a masterclass in riding in wet conditions to finish with a time of one minute 9.782 seconds, overtaking Carlos Checa at the front of the grid.

Alex Barros of Honda will start from second with world championship leader Valentino Rossi is in third.

Britain's Neil Hodgson qualified in 12th place on his Ducatti.

Bryne crashes in practice

Shane Byrne did not compete in Saturday's session after dislocating his wrist in a crash in practice.

The Aprilia rider was thrown from his bike at high speed but escaped with bruising to his legs and the dislocated left wrist, which seem likely to keep him out of the race. His Northern Ireland team colleague Jeremy McWilliams qualified in 14th.

"We are not 100% ready if it's dry for the race but we made big progress in the wet," said Gibernau.

"Hopefully if it's dry we will find a good set-up in the warm-up on Sunday."

Checa, who was in provisional pole after a good ride in Friday's first qualifying, slipped to sixth and a fortunate escape from his high-speed crash.

MotoGP - second qualifying:

1. Sete Gibernau (Spain) Honda 2 hours 09.782 secs
2. Alex Barros (Brazil) Honda 2:10.090
3. Valentino Rossi (Italy) Yamaha 2:10.470
4. Troy Bayliss (Australia) Ducati 2:10.923
5. Colin Edwards (U.S.) Honda 2:11.096
6. Carlos Checa (Spain) Yamaha 2:11.188
7. Nicky Hayden (U.S.) Honda 2:11.662
8. Max Biaggi (Italy) Honda 2:11.737
9. Loris Capirossi (Italy) Ducati 2:11.821
10. Ruben Xaus (Spain) Ducati 2:12.073