Ferrari's woes continued with Kimi Raikkonen retiring before the start of Sunday's Malaysian Grand Prix and teammate Sebastian Vettel starting from the back of the grid after engine problems on Saturday.
With just six of the 20 rounds remaining, the gap between Hamilton and Vettel - who had led until only two races ago - is the biggest it has been so far this season.
The mishap was even stranger, given that Ferrari had looked very strong in the third and final practice earlier Saturday with Raikkonen leading from Vettel.
Raikkonen, who was behind Vettel in a Ferrari one-two during Friday practice, reversed the finishing positions when he set a time of one minute, 31.880 seconds around the Sepang Circuit.
Sunday's race is live on the BBC Sport website and radio 5 live at 08:00 BST.
Hamilton then starts from his 70th career pole position, having edged out Kimi Räikkönen by the narrowest of margins.
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Hamilton had endured a torrid Friday as his Mercedes took a dislike to an aerodynamic upgrade package.
With Hamilton setting a slower time in FP3 and no obvious difference in the data, Mercedes opted to stick with the split aero packages for qualifying to avoid an overhaul of each car's setup.
The first blow went to Lewis Hamilton and Mercedes as he put in an impressive 1.30.076, over two tenths quicker than Raikkonen in 2nd, who could only manage a 1.30.308. I think it's much better if your time and energy is spent looking forward.
Starting from the back of the grid, Sebastian Vettel has a full selection of fresh tyres available and is hoping that gives him strategy options to use his Ferrari - quickest vehicle on the grid - to move through the field.
He returned to the pits but the team ran out of time to diagnose the problem, let alone fix it.
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"We had such a hard day yesterday (Friday), did not know where we stood and did not know whether we could fix the issue, it was hard to sleep", said Hamilton.
"There is a fundamental issue in the vehicle that we need to find out". It is what it is.
"It's part of motor racing", Vettel told Sky Sports.
"Red Bull looked very fast in the mixed conditions this morning, in the damp and wet on the intermediate tyres. I'm in pretty good form", he said. "With a quick auto, you can come back, and overtaking is possible here".
"It's been a hard day but the guys were phenomenal fixing the auto, changing the engine in just two hours". We came here and made big changes with the auto, but the lap was very nice.
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Kvyat's average deficit to Sainz this year over the previous races was 0.173secs.
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