Sebastian Vettel and Ferrari need to overturn a 50-point deficit with only five races remaining and Mercedes' early pace at Suzuka suggested the fight for supremacy this season could be about to reach a tipping point.
Hamilton was nearly half a second clear of the field in both sessions, with title rival Sebastian Vettel unable to get anywhere near the Mercedes.
Meanwhile, Red Bull's Max Verstappen went fourth fastest in the afternoon, more than a second off Hamilton's time with Ferrari's Kimi Raikkonen fifth.
"This track is awesome - I'm having the best day".
Suzuka is one of the drivers favourite tracks and Bottas explains that it is due to how much on the edge you are with one mistake having big consequences.
The 5.8-km Suzuka circuit's unique figure-of-eight layout with its fast, undulating sweeps is a firm favourite with the drivers.
"The auto also felt quite good, although for me it was better in FP1 than in FP2".
"Sorry, but I don't think it's true; I don't think we lost direction".
"I really didn't know where we were going to stand alongside the Red Bulls and the Ferraris", the 33-year-old Briton said after the session.
"We are working so hard to fine-tuning this auto, which we are becoming accustomed to now and as I said I'm loving driving more than ever".
The race begins at 6.10am on Sunday, October 7 with build-up from 4.30am.
Hamilton's pace continued the impression that Mercedes have made a dramatic step forward in performance following the end of the European season.
"In the morning they were quicker through nearly every corner but they had a softer tyre".
Hamilton added: "I'm just loving driving more than ever; when you get in the auto, it's just the best, it's so fast and I'm so grateful to have the opportunity to do what I do. We couldn't do that today but it doesn't matter what they do, we look at ourselves and try to get the best from our package".
"Also, in Russian Federation, it seemed that we were a lot ahead of everyone else on Friday, but in qualifying it gets more intense. I am just grateful for the races I have had and how a lot of then have panned out". "If we can grasp pole, great, but if not we need to be right behind". "Today I think we were both sliding a little bit too much and therefore damaging the tires a bit more than others", he added.