Nicky Hayden set the pace in a wet opening practice session for MotoGP's 2012 finale at Valencia.
A late rally allowed him to work his way down to a 1m44.485s, over one second clear of the field, although the soaked surface was far from conducive to chasing outright times.
Dani Pedrosa had been fastest with two minutes to run, but was in the pits and therefore unable to respond as Hayden made his charge.
The Honda rider, twice a winner at the Spanish track, had to settle for second, 1.005s down.
Newly crowned double-champion Jorge Lorenzo was four tenths down the road in third, ahead of Tech 3's Andrea Dovizioso.
Valencia will mark the Italian's final race with the satellite Yamaha squad before he moves across to Ducati.
Stablemate Cal Crutchlow had held the intra-team advantage when he moved into third with nine minutes to run, but with a flurry of late improvements found himself pushed down to eighth at the flag.
Separating him and Dovizioso were Gresini's Alvaro Bautista, CRT points leader Aleix Espargaro and the second Ducati of Valentino Rossi.
Rossi, like Dovizioso facing his last race for his current team, was just over two seconds down on Hayden.
The second CRT Aspar of Randy de Puniet beat Phillip Island race winner Casey Stoner to ninth.
Despite the conditions there were only two fallers - James Ellison and Katsuyuki Nakasuga, who is replacing the injured Ben Spies this weekend. Both were unhurt.
Pos Rider Team/Bike Time Gap
1. Nicky Hayden Ducati 1m44.485s
2. Dani Pedrosa Honda 1m45.490s + 1.005s
3. Jorge Lorenzo Yamaha 1m45.945s + 1.460s
4. Andrea Dovizioso Tech 3 Yamaha 1m46.021s + 1.536s
5. Alvaro Bautista Gresini Honda 1m46.413s + 1.928s
6. Aleix Espargaro Aspar Aprilia 1m46.574s + 2.089s
7. Valentino Rossi Ducati 1m46.678s + 2.193s
8. Cal Crutchlow Tech 3 Yamaha 1m46.839s + 2.354s
9. Randy De Puniet Aspar Aprilia 1m47.039s + 2.554s
10. Casey Stoner Honda 1m47.527s + 3.042s
11. Stefan Bradl LCR Honda 1m47.825s + 3.340s
12. Karel Abraham Cardion Ducati 1m47.862s + 3.377s
13. Katsuyuki Nakasuga Yamaha 1m48.110s + 3.625s
14. Michele Pirro Gresini FTR-Honda 1m48.244s + 3.759s
15. Ivan Silva Avintia FTR-Kawasaki 1m48.918s + 4.433s
16. Danilo Petrucci Ioda Suter-BMW 1m49.143s + 4.658s
17. Hector Barbera Aspar Ducati 1m49.444s + 4.959s
18. Colin Edwards Forward Suter-BMW 1m49.748s + 5.263s
19. James Ellison Paul Bird Aprilia 1m50.735s + 6.250s
20. Roberto Rolfo Speed Master Aprilia 1m51.826s + 7.341s
21. Claudio Corti Avintia Inmotec-Kawasaki 1m51.996s + 7.511s
22. Hiroshi Aoyama Avintia FTR-Kawasaki 1m54.245s + 9.760s