The Mercedes driver and reigning world champion set a fastest time of 1min 49.834sec, ahead of Ferrari's Sebastian Vettel, after rain halted qualifying for 35 minutes.
The commanding drive from Hamilton, hit by mechanical problems this week, will fuel his charge towards a second race win after he dominated the season-opener in Australia.
Vettel was the day's other big winner and he whooped and hollered to his team as he seized second place from Mercedes' Nico Rosberg in the dying seconds.
"It was a fantastic job for the team to have us both (Hamilton and Rosberg) up here again," a delighted Hamilton said.
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Thunder rumbled overhead, lightning was seen in the distance and dark clouds rolled over the Sepang circuit as Hamilton and Rosberg led the field in Q1.
But McLaren's stormy start to the year showed no sign of easing as former world champions Jenson Button and Fernando Alonso were among the five drivers to miss the cut into Q2.
"Unfortunately Kimi we are P11 and with the rain it will be impossible to improve on that position," Ferrari informed the Finn over the team radio.
Mechanics mopped the pitlane while the Q3 shoot-out was delayed and when the rain finally eased, the cars emerged on a variety of tyres.
Hamilton shot to the top of the board, more than a second quicker than Rosberg, before the team-mates and fierce rivals both pitted for a fresh set of intermediate tyres.
"I just didn't drive well enough, I'm annoyed by that," Rosberg frowned. "Third place is not good enough."
Rain has played spoiler in Malaysia before. In 2012, the race was halted for nearly an hour and in 2009, it lasted just 31 laps before being stopped and awarded to Button.
Weather conditions could again shake up Sunday's Grand Prix, although an earlier start of 3:00 pm local time is thought to ease the chances of another rain interruption.