The Dutch driver had been fastest throughout all three practice sessions at Suzuka and saved the best for qualifying, lapping with a final effort of one minute, 28.877 seconds.
Australian rookie Piastri joined him on the front row but was a massive 0.581 off the Dutchman's time.
Verstappen, whose record run of 10 wins in a row ended in Singapore last weekend when he finished fifth, was the only driver to lap in the 1:28s and said it had been an incredible weekend so far.
"We had of course a bad weekend in Singapore but I already felt from the preparation we had that this was going to be a good track," he said.
"You never really know how good it's going to be but from lap one it has been really, really nice, ... to be on pole here is fantastic."
Red Bull boss Christian Horner, whose team are set to secure the constructors' title on Sunday for a second year in a row even if Verstappen will have to wait for his third drivers' crown, marvelled at what he had seen.
"I think what we've witnessed today is something very special," he told Sky Sports television.
"That first sector was absolutely mighty. That first run looked good enough to get the job done but then he just went quicker again. All his laps have been stunning today ... it's been an absolutely mind-blowing performance."
Piastri said he could have done a better job at the last chicane but it had been a good weekend with an upgraded McLaren.
"It's the first time I've started on the front row for a while, it will be cool" he siad, who sat out last season as Alpine reserve after winning the Formula Two title in 2021.
"There is only one car ahead to try and overtake so I'll try and make that happen."
McLaren's Lando Norris qualified third with Ferrari's Charles Leclerc fourth.
Mexican Sergio Perez, Verstappen's closest title rival and teammate but a massive 151 points adrift after 15 of 22 rounds, qualified fifth.
Red Bull, whose run of 15 wins in a row ended in Singapore last weekend, are set to retain their constructors' title on Sunday but Verstappen will have to wait until at last the next race in Qatar to seal his third championship.
