The championship leader, who needs just one more point to secure back-to-back titles, was there to steal pole by just 0.009s with a time of 1m30.466, ahead of McLarenâ€™s Jenson Button, who had dominated free practice.
In the sister McLaren, Lewis Hamilton was third quickest with a 1m30.617, despite topping the timesheets early in Q3 as he botched his final run leaving him unable to complete a final flying lap.
â€œWhat a qualifying,â€ Vettel said. â€œYesterday I went off in free practice and damaged the wing, so it wasnâ€™t ideal in the afternoon to prepare the car for today.
â€œWe suffered a bit this morning in particular where we were kind of coming back regarding car balance but we were too slow.
â€œWe sat down after the practice session this morning and fortunately got everything together and were able to get every single bit out of the car in qualifying.
â€œIt was crucial, thereâ€™s not much between Jenson Button and myself. It was a tough qualifying, but I enjoyed it a lot. It is a long lap, you have a mega first sector, every time it is a challenge, itâ€™s hard to get it right. I had a bit of a wobble in the first sector but got it right in the second sector.â€
Ferrariâ€™s Felipe Massa out-qualified team-mate Fernando Alonso as the Italian team took fourth and fifth ahead of Red Bullâ€™s Mark Webber, who despite setting the quickest time in sector one, was seven tenths slower than his team-mate.
Michael Schumacher was seventh, ahead of Renault duo Bruno Senna and Vitaly Petrov, and Sauberâ€™s Kamui Kobayashi, as the four drivers opted not to stay in the garage and save tyres in Q3.
The Japanese driver had topped the timesheets in Q1 ahead of Force Indiaâ€™s Adrian Sutil, but with race performance at Suzuka likely to come down to tyre management, only the front runners felt compelled to run at all in Q3.
Sutil missed out on the final session by just eight hundredths of a second as he qualified 11th ahead of team-mate Paul di Resta, who was three tenths slower.
After a disappointing day in Friday practice, Williams found some pace as Rubens Barrichello and Pastor Maldonado qualified 13th and 14th respectfully.
Toro Rosso gambled with saving tyres in Q2 after good early running, and were shunted down to the eighth row of the grid as SÃ©bastien Buemi and Jaime Alguersuari sat in the garage.
Sauberâ€™s Sergio PÃ©rez was troubled by a hydraulic problem, and will start 17th after being unable to set a Q2 time.
Lotus kept up their control as the best of the backmarkers over Virgin as Belgian rookie JÃ©rÃ´me d’Ambrosio out-qualified Timo Glock.
Mercedes Nico Rosberg was the biggest casualty as a hydraulic issue prevented him from running at all leaving him to start 23rd, while HRTâ€™s Tonio Liuzzi was also unable to set a time, and will start 24th and last.
1 Sebastian Vettel (Ger) Red Bull-Renault 1min 30.466secs
2 Jenson Button (Gbr) McLaren-Mercedes 1:30.475
3 Lewis Hamilton (Gbr) McLaren-Mercedes 1:30.617
4 Felipe Massa (Bra) Ferrari 1:30.804
5 Fernando Alonso (Spa) Ferrari 1:30.886
6 Mark Webber (Aus) Red Bull-Renault 1:31.156
7 Michael Schumacher (Ger) Mercedes GP 1:32.116
8 Bruno Senna (Bra) Renault 1:32.297
9 Vitaly Petrov (Rus) Renault 1:32.245
10 Kamui Kobayashi (Jpn) Sauber 1:32.380
11 Adrian Sutil (Ger) Force India-Mercedes 1:32.463
12 Paul Di Resta (Gbr) Force India-Mercedes 1:32.746
13 Rubens Barrichello (Bra) Williams-Cosworth 1:33.079
14 Pastor Maldonado (Ven) Williams-Cosworth 1:33.224
15 Sebastien Buemi (Swi) Toro Rosso-Ferrari 1:33.064
16 Jaime Alguersuari (Spa) Toro Rosso-Ferrari 1:33.427
17 Sergio Perez (Mex) Sauber 1:34.704
18 Heikki Kovalainen (Fin) Lotus-Renault 1:35.454
19 Jarno Trulli (Ita) Lotus-Renault 1:35.514
20 Jerome d’Ambrosio (Bel) Virgin-Cosworth 1:36.439
21 Timo Glock (Ger) Virgin-Cosworth 1:36.507
22 Daniel Ricciardo (Aus) Hispania-Cosworth 1:37.846
23 Nico Rosberg (Ger) Mercedes GP
24 Vitantonio Liuzzi (Ita) Hispania-Cosworth
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