In a repeat of Tuesday's lead order, Honda's Pedrosa very narrowly edged out Yamaha rival Jorge Lorenzo.
This time the gap between Pedrosa's 2m00.549s and Lorenzo's best effort was just 0.019 seconds.
Pedrosa's new team-mate Marc Marquez kept himself in the mix again with third, 0.254s off the pace and 0.235s clear of Valentino Rossi on the second Yamaha in fourth.
Cal Crutchlow fended off Stefan Bradl and Alvaro Bautista to take fifth.
Crutchlow's rookie Tech 3 team-mate Bradley Smith got up to speed on day two, jumping to eighth, 0.6s off his compatriot.
Smith beat the two factory Ducatis, although Nicky Hayden at least got the gap to the front down to 1.5s, a half-second improvement on Tuesday's worrying performance.
Aleix Espargaro led the CRT pack for Aspar. Further back in this group, rookie Michael Laverty was an encouraging seventh 'in class' as he got to grips with Paul Bird's Aprilia, while a neck injury limited Colin Edwards' running.
Results
1. Dani Pedrosa Honda 2m00.549s
2. Jorge Lorenzo Yamaha 2m00.568s + 0.019s
3. Marc Marquez Honda 2m00.803s + 0.254s
4. Valentino Rossi Yamaha 2m01.038s + 0.489s
5. Cal Crutchlow Tech 3 Yamaha 2m01.311s + 0.762s
6. Stefan Bradl LCR Honda 2m01.369s + 0.820s
7. Alvaro Bautista Gresini Honda 2m01.729s + 1.180s
8. Bradley Smith Tech 3 Yamaha 2m01.931s + 1.382s
9. Nicky Hayden Ducati 2m02.110s + 1.561s
10. Andrea Dovizioso Ducati 2m02.379s + 1.830s
11. Kosuke Akiyoshi Honda 2m02.526s + 1.977s
12. Katsuyuki Nakasuga Yamaha 2m02.701s + 2.152s
13. Ben Spies Pramac Ducati 2m03.002s + 2.453s
14. Wataru Yoshikawa Yamaha 2m03.156s + 2.607s
15. Andrea Iannone Pramac Ducati 2m03.169s + 2.620s
16. Aleix Espargaro Aspar Aprilia 2m03.251s + 2.702s
17. Randy de Puniet Aspar Aprilia 2m03.791s + 3.242s
18. Danilo Petrucci Ioda Suter-BMW 2m04.284s + 3.735s
19. Takumi Takahashi Honda 2m04.559s + 4.010s
20. Hirosi Aoyama Avintia FTR-Kawasaki 2m04.786s + 4.237s
21. Hector Barbera Avintia FTR-Kawasaki 2m04.989s + 4.440s
22. Karel Abraham Cardion Aprilia 2m05.028s + 4.479s
23. Michael Laverty Paul Bird Aprilia 2m05.417s + 4.868s
24. Claudio Corti Forward FTR-Kawasaki 2m05.721s + 5.172s
25. Yonny Hernandez Paul Bird Aprilia 2m05.837s + 5.288s
26. Colin Edwards Forward FTR-Kawasaki 2m06.205s + 5.656s
27. Bryan Staring Gresini FTR-Honda 2m06.898s + 6.349s
28. Lukas Pesek Ioda Suter-BMW 2m21.512s + 20.963s
