Russell pipped seven-time world champion Hamilton to the quickest time as Formula One returned to Suzuka for the first time since 2019.
The changeable conditions had seen Mick Schumacher crash out after the chequered flag had already waved to end first practice, with his Haas damaged enough to rule him out of the 90-minute second session.
Nicholas Latifi, Carlos Sainz, Yuki Tsunoda, Charles Leclerc and Sergio Perez all had trips off the track as the rain came and went.
With a high chance of showers during Sunday's race, there was plenty of running in preparation and Mercedes set the pace.
Champion-elect Max Verstappen showed his potential pace for what could prove to be a title-winning weekend with some scintillating laps when the weather allowed.
He managed the third-fastest time in second practice, finishing 0.851 seconds adrift of Russell, with the sister Red Bull of Perez fourth.
Kevin Magnussen was fifth for Haas with Sainz sixth and Fernando Alonso, who had gone fastest for Alpine in the earlier session, seventh.
Valtteri Bottas, the winner last time F1 raced here three years ago, Esteban Ocon and Zhou Guanyu rounded out the top 10.
Verstappen will seal back-to-back drivers' championship if he wins and sets the fastest lap on Sunday.
He was trading fastest laps with Hamilton before Russell posted a time of one minute, 41.935 seconds.
There were only 19 runners in a second session which had been extended to 90 minutes to allow a test of the Pirelli tyres that will be used for the 2023 season - although those plans were scrapped due to the inclement weather.
The rain had earlier put pay to Schumacher's day as he crashed out on his way back to the pits after first practice - not an ideal start to the weekend for a driver whose seat for next year remains under threat.
Third practice and qualifying are expected to take place in the dry on Saturday but rain could return before the lights go out for the start of the race on Sunday afternoon.