The Silver Arrows have claimed one-two finishes at both grands prix so far this year and they were again ahead of the field in dry conditions in Suzuka.
The 19-year-old Italian Antonelli became the youngest pole-sitter in F1 history two weeks ago in China and he made it two in a row with a fastest lap of 1min 28.778sec.
Early championship leader Russell was second 0.298sec behind, with McLaren’s Oscar Piastri third and Ferrari’s Charles Leclerc fourth.
“Super-happy with the session, it was a good one, it was a clean one,” said Antonelli, who won in Shanghai for his maiden grand prix victory.
“I felt very good in the car and every run was improving.”
Russell said he was struggling with his car for most of the qualifying session but still had enough pace to get the job done.
“We were both really fast all weekend, we made some adjustments and then at the beginning of the qualifying we were nowhere,” said the Briton.
“Race is tomorrow and still a lot to play for.”
McLaren’s world champion Lando Norris was fifth, followed by Ferrari’s Lewis Hamilton and Alpine’s Pierre Gasly.
Max Verstappen, who has won the Japanese Grand Prix for the past four years, dropped out in Q2 and will start 11th on the grid.
Red Bull’s Verstappen, a four-time world champion, took pole last year with a track-record lap time.
Verstappen, who crashed out in Q3 in the season-opener in Australia, said his car was “completely undriveable”.
“The car never turns mid-corner and we oversteer a lot on entries,” the Dutchman said.
“It is really difficult, unpredictable.”
Esteban Ocon of Haas, Audi’s Nico Hulkenberg, RB’s Liam Lawson, Alpine’s Franco Colapinto and Williams’ Carlos Sainz also went out in Q2.
Haas driver Ollie Bearman was a shock faller in Q3 after he finished fifth at the Chinese Grand Prix.
Cadillac pair Sergio Perez and Valtteri Bottas went out with him, as did Williams’ Alex Albon and Aston Martin’s Fernando Alonso and Lance Stroll.
The Aston Martin pair, who have yet to complete a grand prix so far this season as they struggle with extreme vibration, finished bottom of the timesheets.
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