Leclerc will join Vettel on the front row for the race later on Sunday, with the grid decided less than three hours before the grand prix after Saturday's running was called off due to Typhoon Hagibis.
Vettel's pole time of one minute 27.064 is a new track record at Suzuka and ended a nine-race run of qualifying behind Leclerc.
Qualifying was hit with further delays as both Robert Kubica and Kevin Magnussen crashed in Q1, putting their participation in the grand prix into doubt.
Nico Hulkenberg ran into a "major problem", later confirmed as a hydraulic leak, which ended his session and further issues for the German came as Antonio Giovinazzi out-qualified Kimi Raikkonen at Alfa Romeo, albeit going out in P11. The Italian is Hulkenberg's main rival if he wants to secure the Alfa seat next season. Daniil Kvyat and Lance Stroll also dropped out.
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