Championship leader Nico Rosberg edged Mercedes team-mate Lewis Hamilton by the finest of margins to grab a third consecutive Suzuka pole position, while Ferrari out-performed rivals Red Bull.
Hamilton had snatched provisional pole on the first runs in Q3, but Rosberg, who had topped all three sections, clocked a 1:30.647 in the dying stages to head his title rival by just 0.013 seconds.
It was an inspired performance from Kimi Raikkonen to take third on the grid behind the Silver Arrows, just three tenths adrift, with Sebastian Vettel setting the fourth fastest time but set to start P7 after receiving a penalty for colliding with Rosberg at Turn 1 last time out in Malaysia.
Max Verstappen therefore climbs to P4, having out-qualified Malaysian GP victor Daniel Ricciardo for just the fourth time since his promotion to Red Bull.
Sergio Perez will line up sixth given Vettel's penalty, with Romain Grosjean a season-best P8 as both Haas cars made into the top-ten shoot-out for the first time in their history.
Nico Hulkenberg and Esteban Gutierrez completed the top ten, out-paced by their respective team-mates.
Williams opted for just a single run in Q2, but neither Valtteri Bottas nor Felipe Massa could deliver the goods and both were knocked out as the Force Indias improved. Bottas will start 11th alongside his team-mate on row six.
The under-pressure Daniil Kvyat took P13 ahead of team-mate Carlos Sainz after the Spaniard spun on his final run Q2, with Fernando Alonso forced to settle for 15th on a miserable day for McLaren on Honda's home turf.
Jolyon Palmer impressively managed to haul his Renault into Q2, but could ultimately do no better than 16th as the top-ten pace Renault showed in FP3 failed to materialise.
Jenson Button, who has struggled throughout the weekend, was the headline casualty of Q1, dumped out by a flurry of late improvements, while Kevin Magnussen also fell at the first hurdle after a costly error through the final sector.
Marcus Ericsson edged Felipe Nasr as Sauber locked-out the penultimate row, with Esteban Ocon out-qualifying Pascal Wehrlein for the second consecutive race at Manor.