Verstappen was in control throughout qualifying and was never really in doubt for pole, but Pérez put together a stunner at the death in Q3 to close to within 0.023 seconds of the Dutchman.
Verstappen’s response was surprisingly flat, opening the gap to just 0.066 seconds - enough for pole, but the slimmest margin between the pair since Pérez took pole at last year’s Miami Grand Prix.
“I think overall his track is very sensitive with the tyres, with the tarmac being really aggressive,” Verstappen said, explaining the slender margin.
“When you go to the limit, it doesn’t always work out. You want every lap to be perfect, but around a track like this it’s not always the case.
“Of course tomorrow is what counts. It’s great as a team to be P1 and P2. Hopefully we can keep that going also for tomorrow.”
Pérez hasn’t qualified for the front row since Miami last year, an astonishing 21 races ago.
The Mexican said he could have gone one better without a scrappy drive through the final chicane.
“It was quite tricky out there actually, especially closing out the lap,” he said. “It was easy to lose a couple of tenths into the chicane.
“I think we’ve been really close all weekend, all the way through qualifying as well. When you’re in those little margins, anything can make a difference.”
Lando Norris qualified an excellent third for McLaren, though the Briton was never in contention for pole, qualifying 0.292 seconds off the pace.
“We’ve had a good weekend,” he said. “We’ve made some good steps forward.
“We’re trying to catch up to these two Red Bulls. The whole team’s doing a good job. We’re working hard, and the hard work is paying off slowly.”
Carlos Sainz struggled with a throttle problem on his way to fourth and 0.485 seconds off the pace, just pipping Fernando Alonso by 0.004 seconds.
Oscar Piastri was sixth quickest on his birthday, the Aussie getting ahead of Lewis Hamilton in the lead Mercedes, which proved the slowest among the five frontrunning teams.
Charles Leclerc burnt through an extra set of soft tyres in Q1 after a scrappy first lap left him vulnerable to a qualifying disaster. It meant he had only one run in Q3, leaving him around 0.1 seconds behind teammate Sainz and eighth on the grid.
George Russell was ninth and ended the session under investigation for an unsafe release early in qualifying.
Yuki Tsunoda will start 10th ahead of RB teammate Daniel Ricciardo, having pipped the Australian for a spot in the top 10 by just 0.055 seconds at his home race, much to the delight of the packed Suzuka grandstands.
Nico Hülkenberg wills tart 12th for Haas ahead of Sauber’s Valtteri Bottas and Thai driver Alex Albon in his Williams.
Esteban Ocon was thrilled to get the struggling Alpine team and its latest upgrades into Q2, but he was slowest of all in that segment never in contention for a high qualification.
Aston Martin’s Lance Stroll was knocked out 16th after a poor performance in his upgraded Aston Martin, leaving almost 0.8 seconds on the table to teammate Alonso.
Pierre Gasly similarly couldn’t wield his upgraded Alpine to break out of Q1, leaving him 17th ahead of Kevin Magnussen, Logan Sargeant – who is driving the repaired chassis crashed by Alex Albon in Australia - and Zhou Guanyu at the back of the field.