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The Dutchman laid down a strong lap early in Qualifying 3, with Perez coming within a tenth of a second as the chequered flag fell.
But while it’s good news for Red Bull Racing with a one-two result, it was a difficult session for Ferrari, with Carlos Sainz fourth and Charles Leclerc only eighth.
Oscar Piastri will line up sixth for McLaren, alongside Fernando Alonso, and three places back from Lando Norris.
Daniel Ricciardo will line up 11th after a hugely promising session, the Australian just half a tenth shy of his team-mate despite less than 30 laps under his belt heading into qualifying.
A queue at the pit exit saw George Russell and Piastri almost make content as the Mercedes driver exited his garage into the path of the McLaren as the qualifying hour begun
The Australian was crawling at the time, so while he reported it to his team as “very dangerous,” it was little more than impolite. Either way, it caught the eye of officials who confirm they’d investigate post-session.
After the initial round of flying laps in Qualifying 1, Verstappen sat fastest ahead of Alonso’s Aston Martin, while Pierre Gasly, Nico Hulkenberg, Logan Sargeant, Kevin Magnussen, and Zhou Guanyu sat in the drop zone.
A second run as the chequered flag waved saw Leclerc climb to fourth, the Ferrari driver one of the 10 on track at the time – Verstappen, Alonso, and Perez were satisfied with their initial effort and remained in the garage.
Ricciardo was on track, improving to ninth and safety with a time that proved 0.05s faster than team-mate Yuki Tsunoda at the end of the segment.
That left the RB duo 10th and 11th while missing the cut were Lance Stroll, Gasly, Magnussen, Sargeant, and Zhou.
Red Bull Racing sent both Verstappen and Perez out in the opening moments of Qualifying 2, but that served to only leave them with traffic as the bulk of the field headed out as they began their flying laps.
Perez logged a 1:28.752s, a time that would prove 0.012s slower than his team-mate, and affording Piastri a slipstream down the front straight in the process.
The McLaren driver used it to bank a 1:29.148s, a time 0.3s faster than he’d managed in Qualifying 1 but quickly bumped from third as Alonso went faster. Norris also bettered his team-mate’s effort.
With his first Q2 run, Ricciardo only mustered a 1:30.873s, close to half a second down on Tsunoda, the pair both in the drop zone with four minutes remaining in the segment.
The leading seven runners didn’t bother with another lap, Leclerc feeling he was safe in seventh with a 1:29.196s.
There was no such luxury at Mercedes, with Hamilton eighth inside the final minute of the session. He climbed to third and Russell seventh, pushing Leclerc to a nervous ninth as others remained on flying laps.
Ricciardo rose to 10th as the chequered flag waved before being bumped to 11th by Tsunoda, to the rapturous applause of the partisan crowd, eliminating his Australian team-mate by 0.055s.
Also out were Hulkenberg, Valtteri Bottas, Albon, and Ocon. Leclerc scraped through in ninth.
Hamilton led proceedings as Qualifying 3 began as nine of the 10 remaining drivers headed out as the 12-minute session began, Leclerc the odd one out.
Hamilton managed a 1:28.766s, a lap quickly obliterated by Verstappen, who clocked a 1:28.240s to move on to provisional pole. Norris came closest with a 1:28.489s to sit second best, with Perez third from Sainz, Piastri, and Hamilton.
As the field filed back into the lane, Leclerc finally emerged on track for his first Qualifying 3 run.
The Ferrari was rapid through the middle sector but off the pace through the opening third of the lap, which left him only seventh. “That’s the best I can do. Honestly, I don’t get it,” he moaned over the radio.
A stunning final lap from Perez saw the Mexican driver challenge Verstappen for pole, but fell short of his team-mate by 0.066s as Red Bull Racing locked out the front row.
Norris remained third from Sainz with Alonso fifth and Piastri sixth. The top 10 was rounded out by Hamilton, a disappointing Leclerc, Russell, and Tsunoda.
The Japanese Grand Prix begins at 15:00 AEST on Sunday.
