Verstappen failed to finish in Australia a fortnight ago but he was in control for the entire race at Suzuka after starting from pole and claimed his third win from four grands prix this season.
The Dutchman finished 12.535sec ahead of the Mexican Perez, who came home in front of Ferrari’s Carlos Sainz in dry, sunny conditions.
Verstappen said “the critical bit was the start, to stay ahead”.
“After that, the car just got better and better,” he said.
“Everything just went very well. It couldn’t have been any better.”
Sainz, who triumphed in Australia, took third ahead of Ferrari team-mate Charles Leclerc, who started from eighth on the grid.
McLaren’s Lando Norris, second in last year’s race, was fifth ahead of Aston Martin’s Fernando Alonso.
Mercedes’ George Russell edged out McLaren’s Oscar Piastri for seventh, while Lewis Hamilton was ninth in the other Mercedes.
Verstappen was starting from pole for the fourth time in as many races this season and stamped his authority on the race from the off, leading Perez to the first turn.
He said this week that Suzuka was one of his favourite circuits and he has now won the Japanese Grand Prix three times in a row.
He was back to his breathtaking best after a brake issue in Melbourne saw him retire from a race for the first time in two years.
“It was a little hiccup the last race but I’m very happy that we’re back on top,” said Verstappen, who has taken an early stranglehold on the world championship.
Perez, who failed to finish at Suzuka last year, picked up his third runner-up finish of the season.
“I think we have a good momentum,” he said.
“Last year here was probably my worst weekend, so I think if we are strong here I think we can be strong anywhere else.
“It’s been a good weekend.”
Japan’s Yuki Tsunoda was 10th for RB, scoring points at his home grand prix for the first time.
Early red flag
The race was red-flagged on only the second lap after RB’s Daniel Ricciardo and Williams’ Alex Albon collided in a frenetic start.
Albon’s front wing clipped into the rear of Ricciardo’s car as they jockeyed for position and both slammed into the wall before getting out unscathed, but their race was over.
The action resumed from a standing start and Verstappen picked up from where he left off ahead of Perez.
Leclerc took over the lead after Verstappen pitted on his 17th lap, but the Red Bull driver was back in front four laps later.
Verstappen and Perez both consolidated their positions, leaving Norris fighting for third against the two Ferraris.
A late lock-up cost the McLaren driver his chance of a podium finish.
Sauber’s Zhou Guanyu retired with a gearbox issue on his 19th lap.
Williams’ Logan Sargeant skidded off the track to a standstill late in the race but resumed driving.
The championship resumes in a fortnight’s time with the Chinese Grand Prix in Shanghai.
It will be the first time the event has been held since 2019, before it was curtailed by the pandemic.
The Japan race was being held in April after being shifted forward from its usual late-season slot.
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