Daniel Ricciardo out-qualified Max Verstappen for only the fifth time this season, but Red Bull Racing look third best in Japan.
Lewis Hamilton shattered the Suzuka track record, set by Michael Schumacher in 2006, to take pole position, with Valtteri Bottas and Sebastian Vettel third.
Ricciardo was fourth fastest with a 1:28.306 - a second slower than Hamilton's pole lap - but will start third because Bottas will take a five-place grid penalty for a gearbox change.
After winning last time out in Malaysia, Max Verstappen was 0.026 seconds slower than his team-mate and was fifth in the session, but will start on the second row alongside Ricciardo.
Championship leaders Mercedes appeared to have struggled in both Malaysia and Singapore before that, despite victory and second place for Hamilton, with Red Bull much closer to the absolute pace, but in Japan, have looked distinctly third best also behind Ferrari.
And while he inherited third place as a result of Bottas' penalty, Ricciardo believes he got everything he could out of the car in qualifying.
"I crossed the line and wasn't shaking my head, but I felt it was all I could get out of it," he said. "Myself and Max pushing each other well at the moment, I'm happy to inherit third and I hope we can run with the leaders.
"The start will dictate a lot, it's hard to overtake here. I've set my car up for the race, so hopefully that will help us."
Verstappen added: "It was ok, could have been better, but we've split our strategies. I've got more downforce than Daniel, and after my first Q3 run I wasn't happy but I was more satisfied with the second run.
"There are a few more fast corners here, which hurts us a bit and it's colder here than in Malaysia. I hope it gets warmer and we get a bit of degradation in the tyres that could help us."