George Russell's car
The 24-year-old lapped the 5.8 km circuit in one minute, and 41.935 seconds in the second session, beating Hamilton's best time by 0.235 seconds on a cold, rainy afternoon.
Red Bull's championship leader Max Verstappen ended the session third fastest.
Russell and Hamilton had ended Friday's opening practice 18th and 13th on the timesheets in a session led by Alpine's Fernando Alonso.
"It’s probably not going to be that representative for this weekend but definitely good learning for the future," said Russell after the session.
"Not a bad afternoon," he added.
Hamilton described the first day of practice as "dull," "grey," and "wet".
"I hope that we will be fast, but that’s a hope that continues to be the case each week," he said.
Verstappen had been sixth quickest in the first session.
The Dutchman heads into the weekend with a 104-point advantage over Charles Leclerc in the overall standings.
With four races remaining after Suzuka, the 25-year-old will be champion for the second year in succession if he leaves Japan with a gap of at least 112 points.
"I just would have liked that it was a little bit more representative," he said.
"In terms of knowing where you are with pace in the wet is always a bit tricky."
Mexican Sergio Perez, winner for Red Bull last week in Singapore, ended the second session fourth quickest, with Kevin Magnussen staying fifth for Haas.
Ferrari's Carlos Sainz, second quickest behind compatriot Alonso in first practice, was sixth fastest in the afternoon ahead of the double world champion.
Valtteri Bottas was eighth quickest for Alfa Romeo ahead of Alpine's Esteban Ocon, China's Zhou Guanyu, with Ferrari's Leclerc only 11th fastest in the second session.
Home hope Yuki Tsunoda, 19th in the morning, improved to 14th in the afternoon.
Mick Schumacher did not take part after crashing his Haas following the opening session, having carried out a practice start.
The German will switch to a spare chassis for the remainder of the weekend.
"Obviously you are trying to figure out the track itself and it’s my first time here, so trying to see where the puddles are because that’s something that is very different in every place you go to," he said.
"Here the water seems to accumulate quite a bit in certain areas and it is a matter of understanding that."
Friday's running at Suzuka was the first Formula One action at the track since 2019, with the venue absent from the calendar for the last two years due to the Covid-19 pandemic.
Schumacher's crash was the only major incident of the day but drivers still struggled to find grip in the treacherous conditions with Leclerc, Perez and Nicholas Latifi, among those who slithered off the track.
The second session ran for 90 minutes instead of the usual one hour to allow drivers to conduct a test of new dry-weather tires. The rain meant the test had to be abandoned but the session still ran for the full 90 minutes.