"I did a couple of mistakes still in my last run but I am very happy because (my) third pole of the year is quite positive," Pedrosa said trackside.
"Normally I don't do so many poles, so I'm happy.
"The track was improving so the lap times were every time faster because (of) no rain today. So we hope tomorrow again to have a dry race.
"Anyway we have to focus for the race and hopefully we can do a good race."
Fifth in the championship, Pedrosa will bid for his second win of the season and first since May in Jerez.
Reigning MotoGP champion Marquez, 33 points ahead of Dovizioso, can sew up his fourth championship with victory on Sunday but will need to do it the hard way.
His effort at Sepang was only the second time in his MotoGP career he has finished outside the top six in qualifying.
Disaster struck at turn 15 of his first lap when he slid off his bike and although he quickly returned to pit, he was unable to make up much ground in a furious finish to the Q2 session.
Between he and Dovizioso are three formidable competitors on the second row, with Italian great Valentino Rossi fourth on the grid for Yamaha ahead of fifth-placed team mate Maverick Vinales and three-times world champion Jorge Lorenzo sixth on his Ducati.
The trio will only be too happy to frustrate Marquez to keep the championship race alive into the final round at Valencia.
(Reporting by Ian Ransom in Melbourne; Editing by Peter Rutherford/Amlan Chakraborty)
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