Verstappen, who failed to finish the race in Australia a fortnight ago, clocked a fastest lap of 1min 28.197sec in dry conditions at Suzuka — just 0.066sec ahead of the Mexican.
It was the fourth time the Dutchman has claimed pole in as many races this season.
“It was quite close at the end,” said Verstappen.
“Overall, this track is very sensitive. When you really want to go to the limit, it doesn’t always work out.”
McLaren’s Lando Norris was third, 0.292sec behind Verstappen.
Perez was in third place heading towards the end of a gripping qualifying session but he almost snatched pole from his team-mate in the dying seconds.
“I think we went really close all the way through,” said Perez.
“When you are in those little margins, anything can make a difference.”
Ferrari’s Carlos Sainz, who won in Melbourne, was fourth.
Aston Martin’s Fernando Alonso was fifth ahead of McLaren’s Oscar Piastri and Mercedes’ Lewis Hamilton.
Ferrari’s Charles Leclerc finished eighth ahead of Mercedes’ George Russell and RB’s Yuki Tsunoda.
Verstappen won the first two grands prix of the season but he retired in Melbourne with a brake issue, marking the first time he had failed to finish a race in two years.
He has looked back to his formidable best so far at Suzuka, topping the time sheets in the first and third practice sessions while sitting out the second because of bad weather.
He followed that up with another dominant performance in qualifying, claiming pole at the Japanese Grand Prix for a third straight year.
“It’s great as a team to be one and two, and hopefully we can keep that going tomorrow,” said Verstappen, who went on to win from pole last year.
Japan’s Tsunoda made it to Q3 with a last-gasp charge, edging out RB team-mate Daniel Ricciardo as well as Nico Hulkenberg, Valtteri Bottas, Alex Albon and Esteban Ocon.
Stewards were set to investigate an early incident where Russell was released into Piastri’s path in the pit lane.
“Very dangerous from Russell,” Piastri said over team radio.
Alpine’s Pierre Gasly was eliminated in Q1 for the fourth time this season.
Lance Stroll, Kevin Magnussen, Logan Sargeant and Zhou Guanyu also fell at the first hurdle.
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