He lapped the 5.8 km circuit in one minute, 41.935 seconds in the second session, beating Hamilton's best time by 0.235 seconds on a cold, rainy afternoon, with Red Bull's championship leader Max Verstappen ending 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.
Verstappen had been sixth quickest.
The Dutchman heads into the weekend with a 104-point advantage over Charles Leclerc in the overall standings.
With four races remaining after Suzuka, he will be champion for the second year in succession if he leaves Japan with a gap of at least 112 points.
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, but that was the only major incident of the day.
With Formula One returning to Suzuka after a two-year absence due to the COVID-19 pandemic, some drivers, including Leclerc, Perez and Nicholas Latifi, slithered off the track in the slippery conditions but escaped unscathed.
The second session ran for 90 minutes instead of the usual one hour to allow drivers to conduct a test of new dry weather tyres. The rain meant the test had to be abandoned but the session still ran for the full 90 minutes.
