The Spaniard, who wrapped up his fifth world title with three rounds to spare in Japan last month, was penalised by stewards for riding irresponsibly in impeding Suzuki's Andrea Iannone.
The move means Marquez, who was found to have been riding slowly on the racing line, will start seventh but retains the pole for the record books.
Yamaha's Zarco had been more than half a second slower than Marquez with a time of two minutes 12.709 seconds around the Sepang circuit.
Seven-times world champion Valentino Rossi, 15 points behind Ducati's Italian Andrea Dovizioso in the race to be overall runner-up in the championship, steps up to second on the grid for Yamaha with Iannone third.
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Dovizioso was one of several riders to crash on Saturday and starts fourth on an all-Ducati second row with Australian Jack Miller and Italian Danilo Petrucci.
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 misses the race after withdrawing on Saturday.
The three-times world champion had wrist surgery after a crash in practice in 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 and Alan Baldwin in London, editing by Amlan Chakraborty and Ken Ferris)
