Hamilton qualified in a time of 1 minute, 24.922 seconds around the Albert Park circuit, a tenth of a second ahead of teammate Jenson Button with Lotus' Romain Grosjean a surprise third.
Most importantly, the McLarens had a two-thirds of a second gap over reigning world champion Sebastian Vettel, who imperiously won 15 poles last season while sweeping to the title. Saturday's results suggested a much tighter contest this season.
Coming into Saturday's session, two-time defending constructors' champion Red Bull had put at least one car on the front row in 24 straight races since the 2010 Italian Grand Prix, but Vettel will start sixth on the grid, one place behind teammate Mark Webber.
"It's a fantastic feeling to be back here, and it's an incredible start to the season," Hamilton said. "It was a tremendous job from the team to get us to this point. We've had a couple of tough years, but we never seem to give up."
Seven-time world champion Michael Schumacher qualified fourth, with Nico Rosberg seventh in the other Mercedes.
However, argument over the legality of Mercedes' wing system continued off the track on Saturday, with Lotus pushing for a definitive ruling from the FIA over the Mercedes system, which channels air from the rear wing to the front wing to increase downforce.
"We have clearly a query on the legality of the Mercedes system," Lotus team principal Eric Boullier said on Sky Sports television. "We have just explained our view to Charlie (FIA technical delegate Charlie Whiting) and we'll wait for Charlie to respond.
"We expect a clarification today or tomorrow, but definitely we would like to fix and understand this position before the next race."
Whiting had already given an initial clearance to the design, and a move to ban the wings on the day of the race was unlikely, but a ruling would be expected before next weekend's Malaysian Grand Prix.
Saturday's challenge was an echo of 2009 in Australia when Red Bull and others unsuccessfully protested the double diffuser of the Brawn team — the forerunner to Mercedes — which went on to win the title.
Williams' Pastor Maldonado qualified an impressive eighth on Saturday, Nico Hulkenberg was ninth for Force India and Toro Rosso's Daniel Ricciardo rounded out the top 10.
Hamilton's pole was the 20th of his career, making him the 13th man in F1 history to reach that mark and moving him level with Alonso and Damon Hill on the all-time list. It was also the first all-McLaren front row since 2009.
Four of the past five winners in Melbourne have started from pole position, boosting Hamilton's hopes going into Sunday's race.
Button said he was "quite surprised" by the gap to the Red Bulls.
"Red Bull are always competitive, we should never forget that, but we are going to enjoy this and hope we have a great race," Button said.
Grosjean's third place was the shock result in his debut at the Albert Park circuit. The Frenchman was expected to spend the season in the shadow of Kimi Raikkonen — who qualified a lowly 18th — but the 2011 GP2 champion showed he had matured since his brief, troubled time in F1 in 2009.
"A few people believed in me in the toughest times and today I am back, almost at the top," Grosjean said.
It was a dismal day for Ferrari, with Fernando Alonso spinning off into a gravel trap early in session two and qualifying in 12th place, while Felipe Massa fared even worse, qualifying 16th.
"We are not quite quick enough," Alonso said. "We need to change the direction quickly if we are to challenge for the championship. We have to react."
Comeback driver Raikkonen also disappointed, qualifying a long way behind teammate Grosjean.
The Finn had struggled on Friday and Saturday with a steering system that did not suit his driving style, and said poor communication from his team caused him to miss out on session two by a tenth of a second, having run wide on his last flying lap.
"I slowed down because we were supposed to have time for one more lap and I guessed we didn't," Raikkonen said. "Nobody told me when I slowed down that I had to hurry up. There's no point to blame anybody and everyone is as disappointed as me. It's a bad start."
Vettel, who set a record for pole positions in a season in 2011, made an error on his last flying lap but said pole position was out of reach regardless.
"McLaren did a massive step from Q2 to Q3," Vettel said. "I should have been a bit better. I made a mistake so that's down to me, probably cost me one or two places."
The HRTs predictably failed to reach the time needed to take part in Sunday's race, with neither car getting within the required seven per cent of the best time in the first qualifying session.
The team, which missed preseason testing and was still putting its cars together on Friday, asked race stewards for an exemption to the rule but were denied, meaning they will be sidelined in Australia for the second straight year.