The Red Bull driver bounced back from a fifth-place finish at last week's Singapore Grand Prix to top the timesheets ahead of McLaren pair Oscar Piastri and Lando Norris.
Verstappen said "Singapore didn't happen" after he roared round the Suzuka circuit in a fastest time of one minute and 28.877 seconds - 0.581 seconds quicker than Piastri.
The runaway championship leader warned there was more to come in Sunday's race, saying he was "very fired up to have a good weekend here".
"As soon as we put the car on the track it's been very enjoyable to drive, very predictable, which I think is the most important," said Verstappen.
"Lap after lap in qualifying was getting better."
Verstappen, who leads teammate and nearest rival Sergio Perez by 151 points in the championship standings, cannot clinch the title on Sunday but a favourable result can set him up to seal the deal at the Qatar Grand Prix next month.
He has won 12 of 15 races so far this season, including a record streak of 10 in a row that ended in Singapore.
He and Perez can help Red Bull clinch the constructors' championship in Japan.
"That was the aim, especially coming from Singapore, I wanted to have a really strong weekend," said Verstappen, who finished fastest in all three Suzuka practices.
"Of course, we know that this is the first proper opportunity to win it."
Verstappen said he was enjoying cutting loose on the sweeping high-speed curves of Suzuka after the tight street circuit of Singapore.
"These high-speed corners are really well-balanced and you can push it to the limit," he said.
"It's just really enjoyable to do."
Piastri power
Piastri claimed second place on the grid with a time of one minute and 29.458 seconds.
The Australian rookie had the third-fastest time in Saturday's final practice before qualifying and said he thought he "could be in for a solid weekend".
"This morning we made some good changes and the car looked quick in FP3, I was getting more used to the track too," said the 22-year-old.
"Very happy to be on the front row. Of course, the gap is a lot bigger than I would prefer but I'm happy to be in second."
McLaren teammate Norris was third fastest, 0.035 seconds behind Piastri.
Norris, who finished second behind Ferrari's Carlos Sainz in Singapore, said it had been "a good day".
"I think we've been strong all weekend," he said.
"We're hoping for an easy race but it's never going to be an easy race around here."
Ferrari's Charles Leclerc qualified fourth ahead of Perez and Sainz.
Mercedes pair Lewis Hamilton and George Russell were seventh and eighth, respectively.
"The car has generally felt nice to drive today - that was a relief as yesterday was a bad day," said Hamilton.
"We typically have at least one suboptimal day each weekend, so Friday was likely that."
Japan's Yuki Tsunoda, who signed a new deal to race for AlphaTauri again next season, qualified ninth in his home grand prix, ahead of Aston Martin's Fernando Alonso.
Liam Lawson, Pierre Gasly, Alex Albon, Esteban Ocon and Kevin Magnussen were all eliminated in Q2.
The first qualifying session was red-flagged when Logan Sargeant crashed his Williams at the final corner.
The American escaped unscathed but his car sustained serious damage after hitting the grass and slamming into the barriers.
Sargeant was eliminated in Q1 along with Zhou Guanyu, Valtteri Bottas, Nico Hulkenberg and Lance Stroll.
