Honda's Dani Pedrosa blazed to pole position for the Malaysian Grand Prix ahead of newly crowned MotoGP world champion Casey Stoner in qualifying on Saturday.

The Spaniard clocked a fastest lap of two minutes, 1.462 seconds on a bumpy Sepang circuit to edge team mate Stoner and claim only his second pole of 2011 for Sunday's race.

Pedrosa is currently fourth in the world championship standings on 208 points, chasing Italian Andrea Dovizioso (212) with two races left this season.

Stoner's best lap was 2:01.491 with Dovizioso's 2:01.666 completing a Honda front row in steamy conditions in Malaysia.

"We can improve a bit before tomorrow but our race pace is okay," Stoner told reporters. "With this humidity and heat over the weekend it's going to be a tough race for sure."

Pedrosa did not have things all his own way despite dominating practice, falling at the final corner just 12 minutes into qualifying.

He quickly rejoined the fray but it took him until 38 minutes into the hour to return to top spot after some jousting between Dovizioso and Marco Simoncelli's Honda.

Dovizioso briefly snatched it back before Stoner, who captured his second MotoGP title at his home Australian Grand Prix last weekend, set a lap 0.061 seconds quicker.

But Pedrosa, who was fourth at Phillip Island, would not be denied and reasserted his authority in the final runs.

Yamaha's Colin Edwards was fourth quickest ahead of Simoncelli and Nicky Hayden's Ducati.

Seven-times MotoGP world champion Valentino Rossi took a spill at turn 10 but jumped on his spare bike to claim ninth to sum up a frustrating first season at Ducati.

Switzerland's Thomas Luthi rode to his maiden Moto2 pole position, while Kalex's world championship leader Stefan Bradl qualified 34 places ahead of title rival Marc Marquez.

Spaniard Marquez, still in pain after crashing on an unflagged wet area in Friday's practice, is three points behind Bradl with two races left but starts 36th on the 37-bike grid.

The Suter rider completed just the required two laps, meaning German Bradl can clinch the title if he wins in Sepang and Marquez is lower than 13th.

Aprilia's 125cc world championship leader Nico Terol claimed pole position on the very last lap by just 0.015 seconds from team mate Hector Faubel.

The Spaniard starts with a 25-point lead over Johann Zarco and will be champion if he finishes ahead of the Frenchman, or Zarco fails to score.

Zarco struggled in qualifying, falling off his Derbi and then pitting for repairs before settling for 15th on the grid.