The Englishman completely smashed the Suzuka track record in Q3 and finished nearly half a second clear (1:27.319) of bitter rival Sebastian Vettel (1:27.791), who qualified in third.
The Ferrari driver battled from the back of the grid at Sepang to finish fourth, two places behind Mercedes' Hamilton, and now sits 34 points adrift of the Briton at the top of the drivers' standings.
Saturday was Hamilton's 10th pole of the season and marked a convincing return to the top of the timesheets for Mercedes after the champions struggled for pace at the last two races in Singapore and Malaysia.
"The last race the vehicle was a disaster, so second place was not too bad", Hamilton said.
It was his first pole at Suzuka, 10th of the season. Vettel and Hamilton were on softs while the rest of the first runners were on super softs.
The team-mate of Ake, Sergio Perez (1 m 51,345 s), and the duo of Williams formed of Felipe Massa (1 m 52,146 s) and Lance Stroll (1 m 52,343 s) were the only other drivers to complete a timed lap during the session was shortened. Bottas made it 1-2 for Mercedes as Vettel qualified third ahead of Ricciardo. This became the first Japanese Grand Prix pole for Hamilton at Suzuka.
"I think it's pretty clear we need to do our best".
'For us normally we are a bit stronger in the race compared to qualifying, so we get together and see what we can do at the start and during the race'.
"This track has always been one of the greatest and with this auto it's just mind-blowing", added the triple world champion, looking to hit back in Japan after being stunned by Red Bull's Max Verstappen in Malaysia last weekend.
'The vehicle balance is getting better and better.
In summary, penalised for using additional power unit components are Sainz (20 grid places), Alonso (35), and Palmer (20). For Sauber driver Pascal Wehrlein (right), it is a time to float, or would that be race, a paper boat down the pit lane, with help from his team mechanic.