The Mercedes driver, and current world champion, beat Ferrari's Sebastian Vettel into second place who himself snatched a front row berth away from countryman Nico Rosberg in the final seconds of qualifying.
"It was a fantastic job for the team to have us both up here again," Hamilton said, referring to teammate Rosberg's third place finish.
Initially it had appeared that the tensions that had marked last season's title race had re-emerged.
Hamilton aborted a flying lap after it looked like Rosberg had blocked him. But both men played down the incident in the post-qualifying press conference.
Rosberg, for his part, was more annoyed that Vettel had managed to steal second place at the death.
"I just didn't drive well enough, I'm annoyed by that," Rosberg said.
"Third place is not good enough."
Qualifying took place amid spectacular thunderstorms which delayed qualifying by half an hour. Indeed, Malaysia has become known for such conditions. The 2012 race was halted for an hour and in 2009 abandoned altogether and awarded to Jenson Button after 31 laps.
But Hamilton made light work of the conditions, looked the quickest throughout and will try to build on his season opening win in Australia.
Yet perhaps the most impressive performance of the day came further down the grid.
Toro Rosso's 17 year old driver Max Verstappen will start the race in sixth in only his second race for the team.