Sebastian Vettel became the third different driver to take a pole position in the first four races of the season. (Reuters Photo)
Vettel's Australian team mate Mark Webber was third quickest and shares the second row with McLaren's Jenson Button.
The pole was the 31st for Vettel, who took a record 15 last season but had failed to get on the front row in the first three races of 2012.
He celebrated his achievement at the desert track, even if there appeared to be few paying spectators present to witness it, with his familiar single finger in the air - a gesture absent so far this season.
"This one I completely owe it to the team," said the champion, who had a scare in the first phase when he dropped dangerously close to the cut-off point after assuming he had done enough.
"The boys, I don't think had much sleep the last four races. It was a tough weekend in China and now here they seriously have a lack of sleep."
The first three races have seen three different winners, without a Red Bull driver on the top step, and Vettel has a good chance of making it four in a race that is going ahead despite worldwide condemnation and calls for it to be cancelled.
"I am very happy with the job that we've done," said Hamilton, who has finished third for three races in a row after poles in Australia and Malaysia. "Probably one of my best qualifying sessions."
Qualifying started as scheduled shortly after news filtered through to an at-times jittery media centre that a protester had been found dead in a rural village after clashes with police on Friday evening.
The pro-democracy protestors, kept at a distance by tight security around the circuit in the south of the island some 30km from Manama, are mostly from the majority Shi-ite Muslim community and blame the Sunni ruling elite for shutting them out of opportunities, jobs and housing.
Members of the Force India and Sauber teams have been caught up in incidents on the highway involving youths throwing petrol bombs and Force India decided to miss second practice on Friday to ensure staff were back in hotels before nightfall.
In what may have been more than a coincidence, the Force India cars were almost invisible on the feed provided by Formula One Management on Saturday, despite Britain's Paul Di Resta qualifying 10th.
Germany's Nico Rosberg, who took his first win after 111 starts at the Chinese Grand Prix last weekend, qualified fifth for Mercedes.
His team mate Michael Schumacher, the seven-times world champion, will start 17th after being slowed by a rear wing problem that allowed Caterham's Heikki Kovalainen to leapfrog him and get into the second session.
Australian Daniel Ricciardo put his Toro Rosso in sixth place, the best qualifying of his fledgling career.
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