The pole was the 57th of Vettel’s career and only second this season.
It also hands Ferrari their fifth pole in a row with Leclerc starting the last four races from the front.
Qualifying took place at a sunny Suzuka on Sunday morning after being postponed from its usual Saturday slot due to the approach of Typhoon Hagibis.
Drivers and teams will now face a quick turnaround with the race set to start as planned at 4.10 pm AEDT.
Vettel, who has come under pressure from the younger Leclerc, has won four times at Suzuka and will be hoping to carry his formidable form into the race later on Sunday.
Ferrari will be hoping to avoid a repeat of the last race in Russia where tensions between their drivers threatened to boil over while they were running first and second.
Mercedes, who have started from pole and won the last five races in Suzuka, have a shot at clinching a record-equalling sixth constructors’ title later on Sunday.
But, needing to score 14 points more than Ferrari to get the job done, the battle will stay alive until the next race in Mexico if they finish as they qualified.
Max Verstappen will start fifth for Red Bull ahead of teammate Alexander Albon with the Red Bull drivers starting engine supplier Honda’s home race from the third row of the grid.