Verstappen who set the pace with a lap of one minute 28.197 seconds, 0.066 seconds clear of Perez, becomes the first driver to take pole in the opening four races of a season since Lewis Hamilton nine years ago.
But with McLaren's Lando Norris, Ferrari's Carlos Sainz and Aston Martin's Fernando Alonso in the other top five spots and all within half a second of Verstappen, Sunday's race promises to be a closer affair than the Dutchman's 2023 procession.
"It was very close in the end," said Verstappen, looking to bounce back from a mechanical issue that prevented him from finishing the race last time out in Melbourne. "Nevertheless most importantly to be on pole - of course you want every lap to be perfect but at a track like this it isn't always the case".
Norris, who finished second in Suzuka last year, will start Sunday's race third on the grid, qualifying 0.292 seconds behind Verstappen.
"We had a good car today, we could fight," said Norris. "We are trying to catch up to the Red Bulls, but they are doing a good job so hats off to them."
While Sainz, who won the last race in Australia after Verstappen's withdrawal, qualified in fourth, his teammate Charles Leclerc had a difficult drive, which will put him back in eighth for Sunday's start.
"That's the best I can do. Honestly, I don't get it," a frustrated Leclerc said over the team radio towards the end of qualifying.
Aston Martin's Alonso and McLaren's Oscar Piastri, celebrating his 23rd birthday, finished in fifth and sixth respectively.
Seven-time world champion Hamilton and George Russell, both of Mercedes, finished in seventh and ninth, but Hamilton sounded optimistic that a season beset by technical problems may be turning a corner.
"It’s actually the first weekend I have not gone crazy with setup... It's been really enjoyable driving. It's just the guys are just a little bit faster," the Briton said.
Mercedes incurred a 5,000-euro ($5,400) fine in qualifying for an unsafe incident after Russell nearly collided with Piastri in the pit lane when exiting his garage.
Local hero Yuki Tsunoda got one of the biggest cheers of the day when he snuck into the final round of qualifying and will start 10th on Sunday.
He once again finished ahead of his more experienced teammate at RB, Daniel Ricciardo, heaping pressure on the Australian driver, whose seat is at risk with the highly regarded reserve driver Liam Lawson waiting in the wings.
"I’m kind of relieved that I'm able to go through to Q3 in front of Japanese fans because I felt slightly more pressure compared to the past three years," said Tsunoda.
"I super enjoyed being in front of the Japanese crowd."
Alonso's Aston Martin teammate Lance Stroll struggled meanwhile and was knocked out in the first round of qualifying. He will start near the back of the grid in 16th.
