The 24-year-old McLaren driver, who failed to start either of the two main grands prix so far this season, lapped the 5.8km Suzuka circuit in one minute, 30.133 seconds on Friday.
Antonelli, fired up from his first Formula One win at the last race in China, was 0.092 seconds off the pace, with championship leader Russell third, 0.205 seconds adrift.
The Mercedes pair had led the times in the first session, with Russell fastest ahead of the 19-year-old Italian. They are separated by four points at the top of the championship standings having won one race each, with Russell also taking the sprint win in China.
The pair have locked out the front row in every qualifying session so far, have finished both Sunday races in one-two formation, and could hand Mercedes their first hat-trick of season-opening one-two finishes since 2019.
Piastri's pace-setting effort capped an encouraging day for McLaren after both their cars failed to start in China. His world champion teammate Lando Norris was third quickest in first practice and fourth in the afternoon.
Piastri was fourth fastest in the earlier session.
Reliability concerns at McLaren linger, however, with Norris spending large parts of both sessions with his car being worked on in the garage.
Ferrari, the closest challengers to Mercedes in the opening two rounds, had Charles Leclerc and Lewis Hamilton fifth and sixth in both sessions.
Red Bull's four-time world champion Max Verstappen was seventh fastest in the opening session and 10th in the second.
Audi's Nico Hulkenberg posted the seventh-quickest time in the second session ahead of Williams driver Alex Albon and the Haas of Oliver Bearman.
Fernando Alonso, who handed his Aston Martin over to the team's third driver Jak Crawford for the opening session, was only 19th fastest at what is a home event for the team's power unit partner Honda.
The Spaniard arrived late to Japan after being at the birth of his first child.
There were no major incidents in either of the two sessions.
Audi's Gabriel Bortoleto and Cadillac's Sergio Perez joined the session late, with work being done on their cars.
Rookie Arvid Lindblad of Racing Bulls put just one lap on the board.
Albon went off into the gravel at the high-speed Degner corners and later collided with the Cadillac of Mexican Sergio Perez in the opening session.
He also briefly stopped on track in the second session due to throttle problems.
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