The Spaniard, who is in his first season in MotoGP, set a time of 2 minutes, 0.011 seconds on his Honda on his last lap when the track dried up after a brief shower.
The 20-year-old's effort bettered the previous track record of 2:00.334 set by double world champion Jorge Lorenzo last year.
Multiple Sepang winner Valentino Rossi of Italy qualified second for Yamaha in 2:00.336 while Britain's Cal Crutchlow was third with 2:00.359.
Lorenzo and fellow Spaniard Dani Pedrosa will line up on the second row of the grid.
Pedrosa topped the first three practice sessions but faded in qualifying.
With four races remaining, Marquez has a 39-point gap over Lorenzo on 278 points. Pedrosa is third on 219 points.
"It was quite difficult (conditions)," Marquez said. "Honestly I did not enjoy the last run as I was cornering at the limit and it was completely wet at two turns.
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"But I know the lap time should be good as it was getting dry in the end. As for tomorrow, it will be a different situation as we can expect rain."
Rossi, a seven-time world champion, was also delighted to grab a spot on the front row.
"Today we got good potential and good setting for the bike, I push a lot and it difficult to control on a few corners," Rossi said.
Esteve Rabat of Spain took pole in Moto2 ahead of Thomas Luthi of Switzerland. Pol Espargaro of Spain was third while current championship leader Scott Redding of Britain will start the race from 10th on the grid.
In Moto3, world championship leader Luis Salom will start from pole position for the third time this season after the Spaniard posted 2:13.867 on his KTM.
Alexis Masbou of France was second while Niccolo Antonelli of Italy completed the front row.
[Associated
Press]
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