Verstappen clocked a blistering lap of 1min 26.983sec in his Red Bull, 0.012sec ahead of championship leader Norris, with McLaren’s Oscar Piastri third.
Verstappen set a new Suzuka track record with his final lap in Saturday’s qualifying, pipping Norris right at the death.
“Each session we kept making little improvements, then the last lap was flat out,” said Verstappen, who has won the Japanese GP for the last three years.
“In a Formula One car around here is insane. This is a proper highlight for us to be back on pole here.”
It was Verstappen’s first pole position of the season.
The Dutchman is still looking for his first grand prix win of the new campaign.
Ferrari’s Charles Leclerc was fourth ahead of Mercedes’ George Russell, with Mercedes’ Kimi Antonelli sixth and RB’s Isack Hadjar seventh.
Ferrari’s Lewis Hamilton was eighth, followed by Williams’s Alex Albon and Haas’s Oliver Bearman.
Norris is looking for his second grand prix win of the season, after triumphing in the season opener in Australia.
He finished second behind Piastri in China a fortnight ago in a dominant start to the campaign for McLaren.
“I’m happy, congrats to Max, he did a good job,” said Norris.
“You have to credit something when it is a lap that good that he must have done. I got everything out of the car today, the gaps are tiny.
“Good but not enough.”
Tsunoda was eliminated in Q2 in a disappointing first qualifying drive for Red Bull after being promoted in place of Liam Lawson last week.
The Japanese driver finished one place behind Lawson, who returned to RB after just two races for Red Bull in a ruthless driver swap.
Verstappen has not looked comfortable this week and he again complained to his team over the radio in Q1.
“I still have the same problem, the tyres are not gripping on the front,” the Dutchman said.
Alpine’s Pierre Gasly, Williams’s Carlos Sainz and Aston Martin’s Fernando Alonso were eliminated in Q2 along with Lawson and Tsunoda.
Sauber pair Nico Hulkenberg and Gabriel Bortoleto, Haas’s Esteban Ocon, Alpine’s Jack Doohan and Aston Martin’s Lance Stroll were all eliminated in Q1.
Doohan’s practice on Friday ended when he crashed heavily into a barrier and mechanics had to work through the night to repair his badly damaged car.
Qualifying was suspended for about eight minutes in Q2 when a small trackside fire broke out as sparks from the cars ignited the grass in the dry conditions.
It was the fifth such incident of the weekend, with the second and third practice sessions also disrupted by fires.
Rain has been forecast for Sunday’s race. (AFP)
