Antonelli leads Mercedes 1-2 as Verstappen suffers qualifying shock
Mercedes have claimed one-two finishes at both grands prix so far in a flying start to the Formula One season and they were again dominant in dry conditions at 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.
Antonelli, who won the first grand prix of his F1 career in China two weeks ago, said it was "a really clean session".
"There's still work to do in these big tracks with the energy, how to find a solution that allows us to push even more and drive without thinking too much," he said.
"But overall I think it was good fun."
Russell was fastest in Friday's first practice but he has trailed his younger team-mate in every session since then.
The British driver said he was struggling with his car for most of qualifying and admitted it was "not ideal" going into Sunday's race.
"I've been really comfortable with the car this whole weekend, it's just in qualifying something didn't quite feel right," he said.
"Let's see tonight, maybe we'll get some answers, maybe I can adjust my driving style to compensate."
'Undriveable' Red Bull
Russell's problems paled into insignificance compared with those facing four-time world champion Verstappen, who exited in Q2 and starts from a lowly 11th on the grid for Red Bull.
The Dutchman, who has won in Japan for the past four years, took pole last year with a track-record lap time.
He has railed against new Formula One regulations that see a 50-50 split between conventional and electrical power, and labelled his car "undriveable".
"The car never turns mid-corner, but at the same time this weekend, it's just oversteering a lot on entry," he said.
"It's really difficult, unpredictable."
Verstappen, who finished sixth in Melbourne and retired from the Shanghai grand prix two weeks ago, added: "We have problems that I cannot explain in detail here."
Verstappen was involved in a public confrontation on Thursday when he ejected a reporter from his news conference.
McLaren's world champion Lando Norris was fifth, followed by Ferrari's Lewis Hamilton and Alpine's Pierre Gasly.
Verstappen's Red Bull team-mate Isack Hadjar was eighth, with Audi's Gabriel Bortoleto and Arvid Lindblad of RB rounding out the top 10.
Piastri will be desperate to make an impact in Sunday's race after missing the first two grands prix of the season.
The Australian said his qualifying session was "pretty well executed" after also finishing fastest in Friday's second practice.
"It's nice to be closer," said Piastri of his third place on the grid.
"I think we're learning more and more about the car and about the power unit every weekend."
Esteban Ocon of Haas, Audi's Nico Hulkenberg, RB's Liam Lawson, Alpine's Franco Colapinto and Williams' Carlos Sainz went out in Q2 with Verstappen.
Haas driver Ollie Bearman, who finished fifth at the Chinese Grand Prix, was a shock faller in Q3 and will start from 18th.
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.