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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.
It was Verstappen's first DNF (did not finish) since retiring from Albert Park in the 2022 race and ended his run of race wins at nine.
Sergio Perez was runner-up under the Jeddah Corniche floodlights, last year's winner taking the chequered flag 13.643 seconds behind his triple world champion teammate who now has a 15-point lead in the standings.
Verstappen senior also denied involvement in the anonymous email.
The Dutch driver took the chequered flag 22.4 seconds clear of his team mate Sergio Perez driving a similar RB20.
The action starts in Bahrain on Saturday.
It may be wishful thinking to expect a big change at the front, with Verstappen only getting better and teammate Sergio Perez posing no threat, but even Red Bull recognise they may never have it so good again.
The pole-to-flag victory, for the fourth year in a row under the Yas Marina floodlights, left the 26-year-old alone in third place in Formula One's all-time list of winners.
Charles Leclerc finished second after starting on pole position, losing and regaining the lead and then losing it again before passing Sergio Perez on the final lap to deny Red Bull a seventh one-two of the season.
The champions have won 19 of the 20 races so far, including the last five in a row