Dani Pedrosa edged out title rival Jorge Lorenzo to set the pace as wet track conditions persisted in the final practice session at Aragon.
The Honda rider made his move in the final two minutes of the session, dropping down to a 2m00.490s.
That was enough to edge out Yamaha's Lorenzo, who had been top since the halfway mark, by just over one tenth of a second.
Ben Spies on the second works Yamaha backed up his chart-topping FP2 pace by claiming third, fractions ahead of the satellite Tech 3 bike of Andrea Dovizioso.
LCR Honda's Stefan Bradl meanwhile claimed fifth, just one thousandth of a second ahead of the second Tech 3 of Cal Crutchlow.
The Briton's session was brought to a premature close when he fell at Turn 12 seven minutes from the end.
Karel Abraham on the satellite Cardion Ducati also fell early on, as track temperatures dropped to a weekend-low.
He was able to return however and climb to seventh, ahead of Ducati's Valentino Rossi.
Teammate Nicky Hayden finished 10th, just over one tenth of a second down on the second works Honda of Jonathan Rea.
Pos Driver Team/Bike Time Gap
1. Dani Pedrosa Honda 2m00.490s
2. Jorge Lorenzo Yamaha 2m00.624s + 0.134s
3. Ben Spies Yamaha 2m00.712s + 0.222s
4. Andrea Dovizioso Tech 3 Yamaha 2m00.727s + 0.237s
5. Stefan Bradl LCR Honda 2m00.823s + 0.333s
6. Cal Crutchlow Tech 3 Yamaha 2m00.824s + 0.334s
7. Karel Abraham Cardion Ducati 2m01.419s + 0.929s
8. Valentino Rossi Ducati 2m01.713s + 1.223s
9. Jonathan Rea Honda 2m01.947s + 1.457s
10. Nicky Hayden Ducati 2m02.123s + 1.633s
11. Alvaro Bautista Gresini Honda 2m02.607s + 2.117s
12. Aleix Espargaro Aspar Aprilia 2m03.336s + 2.846s
13. Yonny Hernandez Avintia FTR-Kawasaki 2m03.622s + 3.132s
14. James Ellison Paul Bird Aprilia 2m03.720s + 3.230s
15. Mattia Pasini Speed Master Aprilia 2m04.020s + 3.530s
16. Colin Edwards Forward Suter-BMW 2m04.162s + 3.672s
17. Danilo Petrucci Ioda Suter-BMW 2m04.555s + 4.065s
18. Randy de Puniet Aspar Aprilia 2m04.612s + 4.122s
19. Hector Barbera Pramac Ducati 2m04.647s + 4.157s
20. Michele Pirro Gresini FTR-Honda 2m05.016s + 4.526s
21. David Salom Avintia FTR-Kawasaki 2m05.898s + 5.408s