This was Pedrosa's fifth pole of the season and the 42nd of the Spaniard's career.
Joining him on the front row will be Jorge Lorenzo, who wrapped up the world title in Australia last month, and Casey Stoner, the 2011 champion who is retiring after Sunday's race.
Yamaha rider Lorenzo was assured the title after Pedrosa crashed out at Phillip Island.
QUALIFYING TIMES
1. Dani Pedrosa (ESP/Honda) 1:30.8442. Jorge Lorenzo (ESP/Yamaha) at 0.351
3. Casey Stoner (AUS/Honda) 0.584
4. Cal Crutchlow (GBR/Yamaha) 0.668
5. Stefan Bradl (GER/Honda) 0.913
6. Andrea Dovizioso (ITA/Yamaha) 0.951
7. Nicky Hayden (USA/Ducati) 1.659
8. Alvaro Bautista (ESP/Honda) 1.741
9. Hector Barbera (ESP/Ducati) 1.761
10. Aleix Espargaro (ESP/Aprilia) 1.990