Marc Márquez's tenth pole position of the season was secured in the 125cc session as the Red Bull Ajo Motorsport rider laid down a best lap of 2'13.398. The 17 year-old, who trails Championship leader Nico Terol by just six points going into Sunday's race, was 0.293s faster than second placed Bradley Smith.
The British rider had looked to be on course for his third pole of the campaign as he led towards the climax of the session, but Márquez first posted a time just five-thousandths of a second better than that of the Bancaja Aspar man before improving to end up almost three-tenths clear.
Smith's team-mate Terol was third at 0.706s off Márquez's time with Pol Espargaró (Tuenti Racing) completing a familiar-looking front row of the grid for Sunday's race.
Efrén Vázquez (Tuenti Racing), Sandro Cortese (Avant Mitsubishi Ajo), Esteve Rabat (Blusens-STX) and Luis Salom (Stipa-Molenaar Racing) secured second-row berths, with Tomoyoshi Koyama (Racing Team Germany), Randy Krummenacher (Stipa-Molenaar Racing), Johann Zarco (WTR San Marino Team) and Danny Webb (Andalucia Cajasol) making up the third line of the grid.
Young Brit Danny Kent (Lambretta Reparto Corse), in only his third GP this season, qualified in an impressive 13th position.
There was a crash during the session for local rider Khairuddin Zulfahmi (AirAsia - Sepang International Circuit Team) who was avoided well by the following Márquez, whilst Simone Grotzkyj (Fontana Racing) also fell towards the end.
The 125cc race gets the Shell Advance Malaysian Motorcycle Grand Prix race day schedule underway at 1pm local time on Sunday.