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. PLACE YOUR TEXT ADVERT BELOW:>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> How I Made Me =N=2.5 MILLION In 7 Days from 2 Common Product I Imported and how you can do the same. Click HERE FOR FREE Details right now Warning To Men: This 3 Foods Is Killing Your Erection. Click Here To Know Them REVEALED!! Reduce Your Blood Sugar Level And Reverse Diabetics Within A Short Period Of Time. Click Here To See How Warning: Got Arthritis? 3 Simple Ways To Get Cured And Be Permanently Free From Joint Pains. Click Here To See Them Secret Fruits that increased my Manhood and makes me last 55 minutes+ all time - Click here to get it MIDNIGHT,Pressed Mr Kilanko Suddenly Couldn't Urinate. Shrink your Enlarged Prostrate Here! Click Here Now