Briton Hamilton, who had been fastest ahead of team mate Valtteri Bottas in first practice, lapped the 5.8-kilometer long Suzuka circuit even quicker in the later session, posting a time of one minute, 28.217 seconds.
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.
Mercedes then locked out the front row in Russian Federation last weekend, where Bottas handed Hamilton the win to make it four victories in the past five races for the Briton.
Vettel has the best record of any current driver at the Honda-owned track, with four wins, but needs a stroke of luck to spark his fading title hopes. "I wasn't totally satisfied with the feeling in the auto today".
"Obviously you don't want to commit suicide, so I think if we attack we will still try to be reasonable. I'm having the best day", Hamilton said after completing his flying laps.
"Every time we come to Suzuka, particularly over the past few years, the cars just get faster and faster", Hamilton said.
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There were 31 passes in the build-up to Alvaro Morata 's stoppage-time strike which put the gloss on a fine 3-0 away win for the Blues .
"But overall, it has been a clean Friday, no interruptions, no issue with the auto or anything", added Vettel.
"When you get in the vehicle it's just the best, it's so much fun and I'm truly grateful to have the opportunity I have". I was much better than I had ever been through those particular corners.
"We'll see how it is in qualifying tomorrow".
"No interruptions, no issue with the vehicle or anything, so now we have to try to obviously squeeze out everything that is left in the auto for tomorrow". "We couldn't do that today but it doesn't matter what they do, we look at ourselves, and we will try to get the best out of our package".
If, as expected, Hamilton takes the chequered flag here on Sunday - a race that he has won in three of the past four years - then there is a small chance that he could secure the championship in America in a fortnight.
"You can always do something, the question is whether it works", Vettel said after FP2, as quoted on Planet F1.
The Mercedes cars have clearly made a step forward in the last couple of races, while Ferrari seemed to have lost their edge.