Jorge Lorenzo was quickest in practice again, despite a violent late crash, as the rain continued at Estoril this morning.
Conditions today were substantially better than Friday morning, but still tough for the riders, and Lorenzo was one of several to make a mistake - being flung from his Yamaha under acceleration at the final corner in the closing minutes.
Despite landing heavily on his back, Lorenzo was unhurt, instantly getting to his feet and walking away.
Just before then, Lorenzo had set a lap of 1m48.853s that would be the fastest of the morning, putting him half a second clear of his team-mate Valentino Rossi.
Andrea Dovizioso grabbed third for Honda with his last lap, pushing Casey Stoner back to fourth. The Ducati rider had a similar accident to Lorenzo on his first run, before rejoining on his spare bike.
Stoner's team-mate Nicky Hayden also fell without injury, in his case at Turn 2, and could not improve on 13th.
Colin Edwards was fifth for Tech 3 Yamaha, ahead of Gresini Honda's Marco Simoncelli and an impressive performance by Pramac Ducati rider Aleix Espargaro in seventh.
The injury-nursing Dani Pedrosa (Honda) and Loris Capirossi (Suzuki) both showed good form in eighth and 10th places, split by Marco Melandri - a pacesetter in the early stages - on the second Gresini bike.
Carlos Checa continued to rue the rain as he tried to get back into the swing of MotoGP with Pramac, though he moved off the foot of the timing screens and was 16th ahead of Aspar Ducati's Hector Barbera.
Pos Rider Team Time Gap
1. Jorge Lorenzo Yamaha 1m48.853s
2. Valentino Rossi Yamaha 1m49.435s + 0.582s
3. Andrea Dovizioso Honda 1m50.007s + 1.154s
4. Casey Stoner Ducati 1m50.081s + 1.228s
5. Colin Edwards Tech 3 Yamaha 1m50.313s + 1.460s
6. Marco Simoncelli Gresini Honda 1m50.500s + 1.647s
7. Aleix Espargaro Pramac Ducati 1m50.787s + 1.934s
8. Dani Pedrosa Honda 1m50.824s + 1.971s
9. Marco Melandri Gresini Honda 1m51.250s + 2.397s
10. Loris Capirossi Suzuki 1m51.518s + 2.665s
11. Ben Spies Tech 3 Yamaha 1m51.916s + 3.063s
12. Alvaro Bautista Suzuki 1m52.734s + 3.881s
13. Nicky Hayden Ducati 1m53.018s + 4.165s
14. Hiroshi Aoyama Interwetten Honda 1m53.317s + 4.464s
15. Randy de Puniet LCR Honda 1m53.537s + 4.684s
16. Carlos Checa Pramac Ducati 1m53.933s + 5.080s
17. Hector Barbera Aspar Ducati 1m54.073s + 5.220s