Hamilton's pole lap of 1:27.319 was over 1.5 seconds faster than the previous record, a 1:28.954 held by Michael Schumacher.
Remarkably, Hamilton's pole position was the first of his career at Suzuka and means he has claimed pole at every circuit currently on the F1 calendar.
"I was very much on it," said Hamilton. "I didn't make one mistake and each lap got better and better.
"It's been 10 years trying to get that pole position!"
Despite being half a second slower than Hamilton, Ferrari's Sebastian Vettel will start the race alongside his world championship rival on the front row.
Valtteri Bottas was second quickest in the session, three tenths down on Hamilton, but will start from seventh due to a gearbox-related grid penalty.
"I tried everything on that last lap as I knew I had to take a bit more risks, it didn't work," said Vettel, who trails Hamilton by 34 points in the standings.
After Mercedes' struggles in Singapore and Malaysia, the world champions have found their groove again in Japan - with Hamilton very much to the fore. SHARE THIS STORY USING ANY OF THE BUTTON BELOW ⬇ PLACE YOUR TEXT ADVERT BELOW ⬇⬇⬇
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