The Formula One championship leader pushed his Mercedes to a time of one minute, 29.599 seconds, just over a tenth quicker than Ferrari rival Sebastian Vettel after a typhoon downpour had forced all 20 cars to dive back into the Suzuka pits.
Lewis Hamilton was probably pretty calm arriving at Suzuka as it was, boasting a 50-point advantage in the drivers' championship over Sebastian Vettel with five rounds still remaining.
The Briton's record-extending 80th career pole never looked in doubt after his rampant form in completing a clean sweep of free practice earlier in the day.
"While it was an anticlimax because I couldn't do the last lap it was my 80th pole".
"It's so hard when the pressure is on to make the right call but that's the big difference between us this year and that's why we're the best and the team deserve it".
With rain threatening, Hamilton clocked a lap of 1 minute, 27.760 seconds to lead teammate Valtteri Bottas by 0.299.
Vettel skidded off twice in his desperation to set a time, and his starting position will be his lowest in a season which began so brightly, but looks like ending in bitter disappointment.
"This is not the position we deserve to be in", insisted the German, who had barely left the garage before informing Ferrari of their mistake over team radio. I think we have better speed than ninth but we'll start there and see how it goes.
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Red Bull's Max Verstappen qualified third, alongside Ferrari's Kimi Raikkonen on the second row. "Is it still a battle?" he asked.
Meanwhile, there were more qualifying woes for Verstappen's Red Bull teammate Daniel Ricciardo, who climbed out of his vehicle and yelled an expletive into his helmet after suffering a mechanical breakdown.
"I lost power as soon as I went to start the lap", said the Australian.
"I do not feel like pointing my fingers at someone in particular, but I'm very disappointed". "I just can't catch a break at the moment".
Esteban Ocon was eighth, ahead of Vettel, with his Force India teammate Sergio Perez rounding out the top 10.
Hamilton controversially took his eighth chequered flag of the season at Sochi last weekend - his fifth win in the last six races - after Mercedes ordered Bottas to give up the lead.
But he has dominated in Suzuka and a fifth victory in Japan would put him on course to clinch the title with races to spare.