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Verstappen crossed the line for his 64th grand prix victory to a huge ovation from the 115,000 crowd, some 1.4 seconds ahead of McLaren's championship leader Lando Norris in second place.
Verstappen recorded a time of one minute 26.983 seconds in the last lap to earn the pole position for Red Bull at Suzuka.
George Russell finished third for Mercedes, ahead of Red Bull's reigning champion Max Verstappen.
Mercedes' George Russell was third on the slippery Albert Park circuit.
The Formula One season-opening Australian Grand Prix will begin on Sunday.
The title gap blew out to 62 points with three rounds remaining and 86 points still to be won.
Verstappen's podium finish left him 57 points clear with five rounds remaining.
It was the McLaren driver's third career GP win.
Verstappen has now failed to win any of the last six GPs after claiming the honours in seven of the first 10.
It was the first time since the race returned to the calendar in 2021 that Verstappen had not triumphed at Zandvoort and extended his losing streak this season to five races.
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