Yamaha's Jorge Lorenzo had become the first man to beat Pedrosa in a 2013 test when he led the way on day two, but Honda was back in front as the Malaysian test wrapped up.
It was a one-two for the team, as Pedrosa's new team-mate Marc Marquez took second place, just 0.081 seconds adrift.
Pedrosa was the pacesetter for most of the session once serious running got underway following morning rain.
Marquez had a minor fall during the day but was soon able to rejoin.
Lorenzo and Yamaha team-mate Valentino Rossi were back in third and fourth, half a second off the pace, as the world champion focused on long runs.
Alvaro Bautista completed the top five on the Gresini Honda, ahead of Cal Crutchlow's Tech 3 Yamaha.
Ducati's tentative progress continued as Andrea Dovizioso got within a second of the pace on the leading works bike in eighth place. His team-mates Nicky Hayden and Michele Pirro both had minor crashes.
Randy de Puniet replaced Aspar team-mate Aleix Espargaro at the head of the CRT pack in 13th overall.
On its second day in action, Paul Bird Motorsport's new in-house chassis got up to 22nd place in the hands of rookie Michael Laverty. Team-mate Yonny Hernandez was back in 26th on the team's Aprilia.
MotoGP's final pre-season test takes place at Jerez on March 23-25.
Times (Rider/Team/Time/Gap/Laps)
1. Dani Pedrosa Honda 2m00.562s 57
2. Marc Marquez Honda 2m00.643s + 0.081s 54
3. Jorge Lorenzo Yamaha 2m00.992s + 0.430s 56
4. Valentino Rossi Yamaha 2m01.062s + 0.500s 61
5. Alvaro Bautista Gresini Honda 2m01.078s + 0.516s 43
6. Cal Crutchlow Tech Yamaha 2m01.094s + 0.532s 59
7. Stefan Bradl LCR Honda 2m01.309s + 0.747s 63
8. Andrea Dovizioso Ducati 2m01.650s + 1.088s 44
9. Nicky Hayden Ducati 2m02.070s + 1.508s 53
10. Bradley Smith Tech Yamaha 2m02.314s + 1.752s 64
11. Andrea Iannone Pramac Ducati 2m02.566s + 2.004s 52
12. Michele Pirro Ducati 2m02.773s + 2.211s 38
13. Randy De Puniet Aspar Aprilia 2m02.863s + 2.301s 45
14. Ben Spies Pramac Ducati 2m03.055s + 2.493s 33
15. Katsuyuki Nakasuga Yamaha 2m03.154s + 2.592s 32
16. Hector Barbera Avintia FTR-Kawasaki 2m03.155s + 2.593s 42
17. Wataru Yoshikawa Yamaha 2m03.257s + 2.695s 26
18. Aleix Espargaro Aspar Aprilia 2m03.423s + 2.861s 45
19. Karel Abraham Cardion Aprilia 2m04.066s + 3.504s 57
20. Colin Edwards Forward FTR-Kawasaki 2m04.102s + 3.540s 42
21. Hiroshi Aoyama Avintia FTR-Kawasaki 2m04.512s + 3.950s 51
22. Michael Laverty PBM-Aprilia 2m04.546s + 3.984s 24
23. Lukas Pesek Ioda Suter-BMW 2m04.674s + 4.112s 33
24. Danilo Petrucci Ioda Suter-BMW 2m04.686s + 4.124s 36
25. Claudio Corti Forward FTR-Kawasaki 2m04.718s + 4.156s 51
26. Yonny Hernandez PBM Aprilia 2m04.722s + 4.160s 47
27. Takumi Takahashi Honda 2m04.749s + 4.187s 65
28. Bryan Staring Gresini FTR-Honda 2m05.313s + 4.751s 40
