Casey Stoner edged MotoGP's Friday morning pacesetter Ben Spies in second practice ahead of this weekend's Portuguese Grand Prix at Estoril.
The pair traded fastest times in the final 10 minutes of a dry second session, before Stoner (Honda) eventually settled the issue with a 1m38.396s - putting him more than three tenths clear of the field.
Spies did enough to claim second, in the process outpacing his Yamaha stable-mate Jorge Lorenzo for the first time this year.
The pair were separated by Tech 3 Yamaha's Cal Crutchlow and the second works Honda of Dani Pedrosa.
Alvaro Bautista put his satellite Gresini Honda sixth, ahead of the two works Ducatis and Hector Barbera's satellite Pramac entry.
Of the trio it was Hayden who emerged on top, with Barbera pipping Rossi to eighth late on.
Rossi finished just over three tenths down on Hayden, but was within 1s of Stoner.
Andrea Dovizioso on the second Tech 3 Yamaha ended 10th, while Aspar's Randy de Puniet was once again the fastest CRT rider in 13th.
Pos Rider Team/Bike Time Gap
1. Casey Stoner Honda 1m38.396s
2. Ben Spies Yamaha 1m38.717s + 0.321s
3. Cal Crutchlow Tech 3 Yamaha 1m38.742s + 0.346s
4. Dani Pedrosa Honda 1m38.797s + 0.401s
5. Jorge Lorenzo Yamaha 1m38.930s + 0.534s
6. Alvaro Bautista Gresini Honda 1m38.959s + 0.563s
7. Nicky Hayden Ducati 1m39.029s + 0.633s
8. Hector Barbera Pramac Ducati 1m39.193s + 0.797s
9. Valentino Rossi Ducati 1m39.357s + 0.961s
10. Andrea Dovizioso Yamaha 1m39.615s + 1.219s
11. Karel Abraham Cardion Ducati 1m40.207s + 1.811s
12. Stefan Bradl LCR Honda 1m40.898s + 2.502s
13. Randy de Puniet Aspar Aprilia 1m41.088s + 2.692s
14. Aleix Espargaro Aspar Aprilia 1m41.634s + 3.238s
15. Yonny Hernandez Avintia FTR-Kawasaki 1m41.638s + 3.242s
16. Mattia Pasini Speed Master Aprilia 1m41.973s + 3.577s
17. Michele Pirro Gresini FTR-Honda 1m42.252s + 3.856s
18. Colin Edwards Forward Suter-BMW 1m42.587s + 4.191s
19. Ivan Silva Avintia Inmotec-Kawasaki 1m42.804s + 4.408s
20. Danilo Petrucci Ioda-Aprilia 1m42.984s + 4.588s
21. James Ellison Paul Bird Aprilia 1m43.665s + 5.269s