Hamilton made it back-to-back poles to start the season, clocking a time that was a tenth of a second faster than teammate Jenson Button, also making it an all-McLaren front row in successive races.
Mercedes driver Michael Schumacher was third fastest, ahead of Red Bull's Mark Webber and Lotus' Kimi Raikkonen, who will take a five-place grid penalty for changing his gearbox and will start Sunday's race tenth.
World champion Sebastian Vettel qualified sixth, Lotus' Romain Grosjean seventh, and Mercedes' Nico Rosberg eighth. Ferrari's Fernando Alonso and Sauber's Sergio Perez completed the top ten.
Rain held off throughout qualifying but is an ever-present threat at Malaysia and could well affect Sunday's race.
Hamilton had a skip in his step as he emerged from the car, in contrast to his post-race demeanour in Australia when he was very disappointed to have finished third after.
"I don't know if (pole) is the best place possible to start here, it's a long haul to turn 1," Hamilton said.
"It's about positioning, it's about tire management. It's a tricky circuit with the track temperatures and the humidity outside — it's going to be tough tomorrow."
Button was again second-best to his teammate in qualifying but the 2009 Malaysia winner will be bolstered by the memory of last weekend in Australia when he beat Hamilton off the line and went on to win the race.
"I can't complain too much — it's good for us as a team to be in the front row," Button said. "You want it the other way around, but Lewis did a great lap at the start."
"It'll be a long, hot afternoon tomorrow but I'm looking forward to it."
Schumacher came within two tenths of his first pole position for six years but Schumacher was enthused by the progress Mercedes is making.
"This was the maximum that was available," the seven-time world champion said. "It's a great achievement. When you think about who is behind us, who would have thought last year?"
Schumacher is a renowned strong starter in races, giving him a good chance of passing the two McLarens in the long drag to the first corner. The Mercedes is the fastest car on the long Sepang straights, but it remains to be seen if the team has cured it's problems in Australia when it was unable to convert qualifying speed into race pace.
Vettel's strategy of qualifying on harder tires will be negated if the tropical rains arrive Sunday and cars switch to wet-weather rubber. But should it stay dry, he could well leapfrog the leaders after the first set of pit stops.
"It's just a different strategy," Red Bull team principal Christian Horner said. "I don't think we had the single lap pace to take on McLaren. In the race we elected to do something different with the two cars so we'll see if it makes a difference tomorrow."
Ferrari improved marginally on a dire qualifying performance in Australia, and Alonso's renowned race craft and the possibility of showers will boost the Italian team's hopes of a good points haul despite its technical deficit in the early part of the season. Felipe Massa qualified 12th.
All 24 cars will start Sunday's race. The HRT cars just squeezed inside the threshold of being within seven per cent of the best time in the first qualifying session, having failed to do so in Australia.Suggest a correction