Verstappen and Pérez started from the front row of the grid and comfortably led away the field from the line, but the race was quickly suspended when Daniel Ricciardo and Alex Albon tangled at high speed at turn 3.
Thai driver Albon was attempting to make a move around the slow-starting Ricciardo’s outside into the fast left-hander at the start of the esses when the Australian drifted to the right, making contact with the Williams.
Ricciardo was tipped into a spin that sent him heavily into the tyre barrier. Albon slipped onto the grass and joined his rival in the wall.
Both drivers walked away from the high speed crash, which the stewards ruled was a no-fault first-lap crash. The barrier, however, was badly damaged, delaying the restart by around half an hour.
The long wait had no effect on Verstappen and Pérez’s plans for domination, with both executing strong starts at the second time of asking to take the lead of the race.
Verstappen quickly took the race into his own hands, eking out an advantage over his teammate that would never be closed to cruise to 12-second victory and average his failure to finish the previous race in Melbourne.
“It was a very, very good win,’ he said. “After the first stint some tiny adjustments were made to the car, and that helped me then to feel even more comfortable. Whenever I needed to go faster, I could. Whenever I needed to look after my tyres, I could.
“That’s always a very nice feeling to have once you’re driving.”
Pérez’s first stint undid any potential bid for victory, with the Mexican uncomfortable on his opening set of medium tyres.
Lando Norris, starting third, seized the opportunity to undercut, making his first pit stop early to gain track position on Pérez when he made his own stop four laps later.
It was only a minor inconvenience. Pérez has been in fine form all weekend, and he made short work of the McLaren with a dive into the chicane to retake second place and complete the team’s third one-two from four races so far this season.
“I think we are in a good momentum,” he said of his strong start to the year. “I think if we are strong in places like this with a lot of high-speed content… I think we can be strong anywhere else. It’s been a good weekend.”
Carlos Sainz completed the podium for the third time this year after a strategic duel with Norris and Ferrari teammate Charles Leclerc.
Norris made his two pit stops early to try to hold track position at a circuit around which passing is historically difficult. Leclerc ambitiously gambled on a one-stop strategy from eighth on the grid, hoping the cooled spring weather would favour him.
Sainz countered with a long middle stint that gave him fresher tyres at the end of the grand. It proved the right call, giving him the pace to sweep past Norris and Leclerc in the final laps to continue building his early-season momentum.
“Very satisfying,” Sainz said of Ferrari’s strong start to the year. “We exactly improved the car in the places that we wanted to improve it, and Suzuka proves it.
“Still at places like Suzuka we are not as quick as the Red Bull, which is the target, but as soon as we bring a good upgrade to the car that goes in the right direction, hopefully it can get us closer.”
Leclerc’s improbable one-stop race at the high-degradation circuit secured him fourth ahead of Norris in fifth.
Fernando Alonso was a clever sixth for Aston Martin after fending off late attacks from George Russell and Oscar Piastri.
Piastri had tailed Alonso through the final stint but was unable to make a move, leaving him vulnerable to a late challenge from Russell.
Russell took five laps to get through Piastri with a last-lap pass into the first corner, by which time it was too late to pursue Alonso, leaving him seventh ahead of his Australian rival.
Lewis Hamilton finished a disappointed ninth and counting the cost of Mercedes’s attempt to make the one-stop strategy work with his unpredictable Mercedes.
Yuki Tsunoda scored the final point of his home grand prix in 10th, the Japanese ace thanking his team for a rapid final pit stop that jumped him ahead of both Kevin Magnussen and Valtteri Bottas in the pit lane.
Nico Hülkenberg finished 11th ahead of Lance Stroll, Magnussen, Bottas, Esteban Ocon, Pierre Gasly and Logan Sargeant. Zhou Guanyu was the race’s only retirement after the first-lap crash, withdrawing from the race with gearbox issues.