Rookie title leader Marc Marquez was black flagged for not pitting within the first 10 laps, meaning his lead has been cut from 43 to 18 points over race winner Jorge Lorenzo.
Phillip Island has been resurfaced since last year's event. Due to tyre overheating issues, the race was the first ever in MotoGP to feature mandatory pit stops.
All riders required to pit and change to their spare bike within 10 laps, while the race distance was reduced to 19 instead of 27 laps.
Honda LCR's Stefan Bradl withdrew after testing his newly fractured ankle in Friday morning practice.
Yonny Hernandez continues to replace Ben Spies at Pramac Ducati, with Damian Cudlin taking over from Hernandez at PBM and World Supersport-ace Scassa replacing the injured Karel Abraham at Cardion AB.
for pictures from the grand prix...
1. Jorge Lorenzo
ESP Yamaha Factory Racing (YZR-M1) 29m 7.155s
2. Dani Pedrosa
ESP Repsol Honda Team (RC213V) 29m 14.091s
3. Valentino Rossi
ITA Yamaha Factory Racing (YZR-M1) 29m 19.499s
4. Cal Crutchlow
GBR Monster Yamaha Tech 3 (YZR-M1) 29m 19.615s
5. Alvaro Bautista
ESP Go&Fun Honda Gresini (RC213V) 29m 19.668s
6. Bradley Smith
GBR Monster Yamaha Tech 3 (YZR-M1) 29m 35.418s
7. Nicky Hayden
USA Ducati Team (GP13) 29m 40.108s
8. Andrea Iannone
ITA Energy T.I. Pramac Racing (GP13) 29m 42.217s
9. Andrea Dovizioso
ITA Ducati Team (GP13) 29m 42.259s
10. Randy De Puniet
FRA Power Electronics Aspar (ART CRT) 29m 44.581s
11. Aleix Espargaro
ESP Power Electronics Aspar (ART CRT) 29m 53.254s
12. Colin Edwards
USA NGM Forward Racing (FTR-Kawasaki CRT)* 29m 55.304s
13. Yonny Hernandez
COL Ignite Pramac Racing (GP13) 29m 57.066s
14. Hector Barbera
ESP Avintia Blusens (FTR-Kawasaki CRT)* 29m 57.153s
15. Danilo Petrucci
ITA Came IodaRacing Project (Suter-BMW CRT)* 30m 5.873s
16. Luca Scassa
ITA Cardion AB Motoracing (ART CRT) 30m 5.946s
17. Claudio Corti
ITA NGM Forward Racing (FTR-Kawasaki CRT)* 30m 15.260s
18. Michael Laverty
GBR Paul Bird Motorsport (ART CRT) 30m 34.385s
19. Lukas Pesek
CZE Came IodaRacing Project (Suter-BMW CRT)* 30m 38.248s
20. Hiroshi Aoyama
JPN Avintia Blusens (FTR-Kawasaki CRT)* 29m 33.585s
21. Damian Cudlin
AUS Paul Bird Motorsport (PBM-ART CRT)* 30m 52.751s
AUS Go&Fun Honda Gresini (FTR-Honda CRT) DSQ
ESP Repsol Honda Team (RC213V) DSQ
* Standard ECU.