In only his third race for the team he joined at the end of last season from McLaren, 2008 world champion Hamilton celebrated the 27th pole of his career at a circuit where he has won twice before.
Ferrari's Fernando Alonso will start third, with Red Bull's Sebastian Vettel ninth and his team mate Mark Webber starting from the back of the grid due to a fuel problem.
"Today is such a blessing to be here up front because it (the move to Mercedes) was such a change for me," Hamilton, last on pole with McLaren at the 2012 Brazilian season-ender, told reporters.
"It's just an incredible feeling. I'm so happy to have our first pole for some time. I'm just ecstatic really. The lap was great."
Mercedes, uncompetitive for most of last season, were last on pole a year ago at the same race with eventual winner Nico Rosberg. The German - whose pole was the first by a Mercedes works driver since 1955 - qualified fourth this time.
Ferrari's Alonso will start ahead of Felipe Massa for the first time this season, denying the Brazilian the honour of being the first team mate to out-qualify the Spaniard for five consecutive races.
"The biggest threat could come from Raikkonen as the Lotus has shown it manages its tyres well," said Alonso.
Massa will start fifth with Romain Grosjean sixth for Lotus.
Red Bull's championship leader Vettel will line up ninth on the grid after opting to start on the slower but longer-lasting medium tyres rather than the new soft compound used by Hamilton.
Vettel did not set a time in the final session after locking a wheel under braking.
"I lost the brake pressure and had to abort the lap," he said.
Webber, barely speaking to the German after Vettel defied team orders in Malaysia and passed him to win, was sidelined by a fuel problem during the second phase of qualifying.
The Australian was 14th fastest but was sent to the back of the grid for having insufficient fuel in the car to drive it back to the pits and provide a mandatory one litre sample.
The governing FIA said in a statement that there was only 150ml left in the tank.
"The amount of fuel that was required to be put into the car from the fuel rig was not fully delivered. This was due to an error with the fuel bowser that meant it under delivered 3kg of fuel," said team principal Christian Horner.
Webber, who had feared a "double-whammy", put a brave face on his situation and agreed it was "not the optimum starting position".
McLaren's Jenson Button, whose car was off the pace in the first two races, found himself in the unexpected position of starting ahead of both Red Bulls in eighth place and on the harder tyre.
"This was the best we could do with what we have," he said. "We don't really have the pace of the front-running cars yet."
There were few thrills in the session as a whole, with the quick-wearing soft tyres creating a situation where drivers opted to preserve their sets for Sunday's race.
The crowd saw no cars at all on the track for the first eight and a half minutes while teams kept the number of laps to the bare minimum.
"These tyres are very tricky this weekend," said Hamilton.
"Making the option tyre last is almost impossible, so it's probably going to be a short stint at the start apart from for this guy (Raikkonen), who seems to be able to look after tyres better than most people.
"But we have good race pace. I expect a tough race but I hope we can maintain position."
Raikkonen, winner of the season-opener in Australia, echoed his thoughts: "I think the gap is quite big still and we don't have that speed right now. So, second is not bad, I think it's the best that I've been with the team ever," he said.
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