The Repsol Honda driver fell on just his fifth lap of the session but rejoined the action to beat team-mates Casey Stoner and Andrea Dovizioso to pole with a time of two minutes 1.462 seconds.
Australian Stoner, who wrapped up the title last weekend, was second, 0.029secs behind, with Dovizioso a further 0.175secs back.
Pedrosa missed the Malaysian Grand Prix last year because he was recovering from a broken collarbone.
And he appeared to be having more bad fortune when he was sent to the tarmac just minutes into Saturday's qualifying session.
It proved to be a minor incident, though, and he went to the top of the tree around 40 minutes into the session.
That proved the start of a three-way battle between the Honda drivers, with Dovizioso then Stoner taking to turns in provisional pole.
But Pedrosa had the final say, putting in the best lap of the day as the session drew to a close.
"I was trying hard for the pole," Pedrosa was quoted as saying on autosport.com. "In one section I was going faster, but then I had some traffic and couldn't improve my lap time.
"But I was still able to be on pole for the second time [in 2011] and that's good, but I'm hoping to do even better in the race."
On the crash, he added: "At the beginning of the session I had a small crash on the front. Then I had to get back on the bike and I was still able to go well."
Colin Edwards (Tech 3 Yamaha) was fourth, ahead of Marco Simoncelli (Gresini Honda) and Nicky Hayden (Ducati).
Great Britain's Cal Crutchlow qualified 10th on his Tech 3 Yamaha.
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