Marquee, who leads the championship by 33 points from Andrea Dovizioso with two rounds to go, will start at his second-worst position of his MotoGP career, after he crashed in turn 15 during his first flying lap. There he had been setting the fastest lap.
He, however, managed to change into his second Honda and finish seventh.
It's only the second time ever in the premier class the reigning champion has failed to qualify in the top six.
"We're not at our best at the moment, but I think our race pace is better then our qualifying position. This morning we made a small mistake with the setup and lost the direction a little bit," said Marquez after the race at the Sepang International Circuit.
"Then we sorted things out and I felt really good on the bike again in FP4, but in qualifying I crashed on my first run, which completely changed our plans."
It would be Pedrosa's third this year, 31st in MotoGP, and the 49th of his career.
He bested Johann Zarco (Yamaha) and Andrea Dovizioso by 0.017 and 0.024 seconds, respectively, in the last minute of an incredibly hard-fought qualifying session.
"I'm very happy with this pole, which is our third this year. Its a nice feeling because I usually struggle in qualifying, but the track improved a lot with today's sunny conditions, offering good grip," Pedrosa said.
Disclaimer: No Business Standard Journalist was involved in creation of this content
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