After a "nightmare" Friday, Hamilton was much happier with his W14 thanks to overnight changes, but he still faced a tricky balance come qualifying.
As high as fourth in Q2, Hamilton took seventh place in Q3, immediately ahead of team-mate George Russell.
The outcome clearly benchmarked the Mercedes as the fourth-best car at Suzuka after the Red Bull, McLaren and Ferrari.
Hamilton admitted that he couldn't have got any more out of the car after some set-up changes overnight.
"I was really much, much happy with qualifying," he noted. "Yesterday, it started off looking like it was not going to be so great! But I think the set-up was in the right direction. And then from P3 to qualifying, I made another setup change.
"And I was really happy with that. But just really hard to pull any more out of it. I'm already on the knife-edge with the rear end the whole way through the lap, all the way through."
He added: "We have a very peaky car. When we talk about knife-edge, it's literally like trying to balance a knife on its tip. And it's that car, it's impossible.
"So it is never perfectly balanced, it's one way or the other, you either oversteer or you've got massive understeer, you can never get in the middle.
"But you try and get it as close as you can to the middle. But it's very, very hard to do each weekend. But once I do get it into a decent place, this is where I qualify."
Hamilton made clear his frustration about being 1.035s off pole man Max Verstappen.
"A second gap is huge, and it's real," he said. "To be two years in [to these rules], and still be a second down, compared to the Red Bulls, it's showing, and we really need to do a good job in the winter to get back at least half that gap before next year."
Mercedes trackside engineering director Andrew Shovlin confirmed that the set-up changes for both drivers focused on the twisty first part of the lap, where change of direction is key.
"We did similar things with both cars overnight," he said. "Trying to focus a bit more on sector one, because we were actually okay in the low speed, and it was sector one where we were very weak.
"The issue with that sector is the more you slide, the more your tyres get hotter. And you are already too hot. So basically, you just get punished if you don't have enough performance there.
"But it's fair to say that yesterday Lewis really didn't feel comfortable with the car. Today, he's a bit better, George looks like relatively he slipped up a bit.
"But I think it was more Lewis just wasn't happy to carry the speed yesterday, and today he has got on with it a lot better."
