Sahara Force India's Nico Hulkenberg qualified 10th but will start Sunday's Japanese Grand Prix from the 15th position on the grid after being handed a five-place penaltly due to an unscheduled gearbox change.
Paul di Resta qualified 12th but will move one place up to 11th, just behind Felipe Massa of Ferrari.
The two Red Bull cars will line up in the front row with defending champion Sebastian Vettel taking the pole position ahead of teammate Mark Webber.
McLaren's Jenson Button was third but a five-place penalty pushes him to eighth.
After managing his fastest lap time in 1:32.272, which was marginally better than his Q1 timing (1:32.828), Hulkenberg did not set a time in Q3 to save tyres keeping in mind the penalty.
"The build-up to qualifying was quite intense because the guys were working hard to repair my car after the accident this morning. It was not a big impact, but the angle was unfortunate and there was quite a lot to fix so all credit to the boys who got me out with enough time to set a time in Q1," he said.
"The car felt good straight away and we made it through to Q3, which was always the target. We then took a strategic decision to save tyres so I didn't set a time. That opens up the strategy for tomorrow, especially because we knew I would get a five-place grid penalty for changing the gearbox," he said.
Paul Di Resta, who got into Q2 with a timing of 1:32.898, improved margninally (1:32.327) but that was not enough to go into Q3.
"It was quite a tough session with traffic today and even on my quick lap in Q2 I was slightly compromised in the second sector. I locked a wheel and it may only have cost half a tenth, but that's how close the margin was to the top ten."
"For tomorrow it's clear that tyre wear will be a big issue for everyone, but hopefully we can use the strategy to challenge the people in front. There are some question marks going into the race because I've done no high fuel running, but we have data with the other car."