The Spaniard, who wrapped up his fifth world title with three rounds to spare in Japan last month, powered around the Sepang International Circuit in two minutes, 12.161 seconds for his 80th pole in grand prix racing.
Marquez was unable to improve on his time because of a late tumble but was still too quick for Yamaha's French rider Johann Zarco (2.12.709) and seven-times world champion Valentino Rossi (2.13.009) who will join him on the front row.
Yamaha's Rossi is 15 points behind Ducati's Andrea Dovizioso in the race to finish second in the championship and his fellow Italian was another of the riders to crash on Saturday, keeping him on the second row of the grid in fifth place.
Torrential rain started falling during the fourth free practice session causing several riders still on slick tyres to fall, including Maverick Vinales who gave Yamaha a first win in 26 races last week in Australia.
Vinales was able to get up and qualify 11th once the safety car came off the track but Jordi Torres was not so lucky and the Spanish Ducati rider broke a finger to be ruled out of the race.
Jorge Lorenzo, who rode through the pain in Friday's practice sessions, is another Spaniard who miss the race after withdrawing on Saturday morning.
The three-times world champion underwent wrist surgery after a crash in practice Thailand, which ruled him out of that race and the following rounds in Japan and Australia. He was replaced by Ducati test rider Michele Pirro, who qualified 14th.
Italian Francesco Bagnaia, who needs to finish fourth or better on Sunday to claim the Moto2 title, qualified sixth just ahead of his closest championship rival Miguel Oliveira.
Because of the potential for more rain, Sunday's programme has been brought forward by two hours with the MotoGP race now starting at 1pm local time (0500 GMT). (Reporting by Nick Mulvenney in Sydney, editing by Amlan Chakraborty)
(This story has not been edited by Devdiscourse staff and is auto-generated from a syndicated feed.)