Valtteri Bottas qualified second fastest but will take a five-place grid penalty meaning Sebastian Vettel, who qualified third, will start alongside his title rival for tomorrow’s race.
Vettel’s Ferrari team-mate will also take a grid penalty after crashing during Saturday morning’s practice session.
Hamilton leads the F1 World Drivers’ Championship by 34 points and will hope to extend that even further with four races remaining after Suzuka.
Bottas’ provisional second place came as a sharp up-turn in the Finn’s fortunes, even if the penalty means he will not start on the front row.
Hamilton’s team-mate has spoken publicly about his disappoitment with fifth place in Malaysia, where he never had the pace to challenge at the front of the race.

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After six consecutive podiums, he has only achieved that feat at two of the last four races but both drivers promised that the car, which struggled with tyre temperatures in Malaysia, is back to its best at Suzuka.
But it did not stop Bottas crashing during FP3 and surviving a big moment on track during qualifying.
However, Mercedes appear to have the best of the pace and Hamilton appeared confident of driving a wire-to-wire victory on Sunday.
“It feels incredible [to get pole],” Hamilton said afterwards.
“It’s been a really good day and every lap was fantastic.
“I never really ever got a great balance here in the past so I never really did a great lap in qualifying.
“So to finally get the balance behind me with the great work of my engineers and the great timing of all the mechanics, we finally got on track and did the time.
“The car is crazy here.
“I thought ‘I’m running out of opportunities to get this pole so I’ve got to make sure I make it stick today!’.”