Testing began at 10am and concluded at 6pm.
Honda riders Casey Stoner, Dani Pedrosa, Alvaro Bautista and Stefan Bradl were returning to action after missing day two while HRC carried out engine checks following a problem on Pedrosa's bike.
Karel Abraham (Cardion AB Ducati) withdrew from the test on day one due to pain from shoulder and back injuries sustained at Jerez last week.
The first two days of testing were both interrupted by rain storms, but only odd drops were reported on Thursday.
Bautista, Ben Spies, Jorge Lorenzo and Nicky Hayden all fell without harm during the final day.
The third and final official pre-season test will be held at Jerez from March 23-25, when the full 21-rider grid - twelve manufacturer bikes plus nine CRTs - will be on track together for the first time.
for pictures from the second Sepang test...
1. Casey Stoner
AUS Repsol Honda 2m 0.473s
2. Dani Pedrosa
ESP Repsol Honda 2m 0.648s
3. Andrea Dovizioso
ITA Monster Yamaha Tech 3 2m 0.802s
4. Jorge Lorenzo
ESP Yamaha Factory Racing 2m 0.877s
5. Cal Crutchlow
GBR Monster Yamaha Tech 3 2m 0.986s
6. Hector Barbera
ESP Pramac Racing 2m 1.231s
7. Alvaro Bautista
ESP San Carlo Honda Gresini 2m 1.275s
8. Ben Spies
USA Yamaha Factory Racing 2m 1.432s
9. Stefan Bradl
GER LCR Honda 2m 1.492s
10. Valentino Rossi
ITA Ducati Team 2m 1.550s
11. Nicky Hayden
USA Ducati Team 2m 1.609s
12. Franco Battaini
ITA Ducati Test Rider 2m 3.490s
13. Colin Edwards
USA Forward Racing (Suter-BMW CRT) 2m 3.681s
14. Yonny Hernández
COL Avintia (FTR-Kawasaki CRT) 2m 6.632s
15. Ivan Silva
ESP Avintia (FTR-Kawasaki CRT) 2m 6.785s
Fastest day two time:
USA Yamaha 2m 1.285s
Fastest day one time:
AUS Honda 2m 1.761s
Fastest Sepang I test times (Feb 2):
AUS Honda 1m 59.607s
ESP Yamaha 2m 0.198s
ITA Ducati 2m 0.824s
USA Suter 2m 4.722s
ESP FTR 2m 8.225s
Official Sepang MotoGP lap records:
ITA Yamaha 2m 0.518s
Fastest race lap:
AUS Ducati 2m 2.108s