The Dutchman suffered his first retirement since 2022 in Melbourne last time out to snap a nine-race winning streak but had no mechanical issues this week in a dominant performance at a sunny Suzuka circuit to make it three wins from four races this season.
"You know it was a little hiccup, of course, the last race but very happy that we are here back on top," said Dutchman Verstappen, who finished 12.535 seconds clear of his team mate and also had the fastest lap.
Verstappen, who becomes only the second driver to win three consecutive Japanese Grands Prix alongside seven-time world champion Michael Schumacher, now has a 13-point lead in the drivers standings over Perez.
Red Bull lead the constructor standings on 141 points ahead of Ferrari (120) and McLaren (69).
"I think we have good momentum," said Perez, who jumped ahead of Ferrari's Charles Leclerc in the drivers standings. "I think if we are strong in places like this with a lot of high speed corners ... we can be strong anywhere else."
Ferrari's other driver Carlos Sainz, the winner in Australia two weeks ago, rode fresher tyres in the latter stages of the race to grab the final podium spot, edging out Leclerc, who used a one-stop strategy.
But the Spaniard was more than 20 seconds behind Verstappen, underlining the gap between teams.
Sainz, who will be replaced at Ferrari next season by Mercedes' Lewis Hamilton, said after the race he was nervous about how the competing strategies with his team mate would work out in the fight for third.
"It was quite tough out there ... I thought that maybe one stop was quicker and we were on the two. I had to overtake a lot of cars out there today," said Sainz.
McLaren's Lando Norris finished fifth with the Mercedes pair of George Russell and Hamilton down in a disappointing seventh and ninth.
Aston Martin's Fernando Alonso finished sixth, with McLaren's Oscar Piastri eighth.
RB's Yuki Tsunoda finished 10th, securing points in his home grand prix for the first time to the delight of the crowd.
"I'm just relieved, that was very long last two years that I wasn't able to score points here," Tsunoda said. "Without the amount of support today and all the week from the fans and the team, I wouldn't be P10. So top job from everyone."
Alex Albon's Williams and the RB of Daniel Ricciardo crashed into each other on the opening lap, triggering a red flag and a 30 minute delay while the debris was cleared and a barrier repaired. Both drivers emerged unscathed.
The wreck is another headache for Williams, who remain without a spare chassis for the next race in China, and for Ricciardo, who is under pressure having underperformed his less experienced team mate Tsunoda this season.
