Sebastian Vettel claimed his fourth successive pole position at the Suzuka circuit, beating Mark Webber to the coveted grid slot.
Vettel has a history of success at the Japanese track, winning the grand prix in 2009 and 2010 and wrapping up his second Drivers' title last season.
That history continued on Saturday afternoon as Vettel posted a 1:30.839 early in Q3 to secure his fourth Japanese GP pole position in a row.
His team-mate Webber ensured a Red Bull lock-out of the front row as he brought his car home 0.251s adrift.
Jenson Button was third ahead of Japan's own Kamui Kobayashi.
The weather had clouded over since FP3 in the morning when the Red Bulls had proved to be the class of the field. The ambient temperature was still high at 26C with the track at 36C.
For the Force India team it was a race to get Nico Hulkenberg's car together after he went off at the Degna turns and crashed heavily in morning practice. However it was team-mate Paul DiResta who was out first setting the initial P1 time at 1:33.661, followed by Kimi Raikkonen 1:33.507 and Romain Grosjean with a 1:33.328.
Felipe Massa looked on fine resurgent form and ducked into the 1:32s with a 1:32.946 - significantly he was faster than team-mate Alonso. Despite drivers setting a time on the harder tyre and then bettering it on subsequent laps - such as Webber, Grosjean, Alonso, Hamilton and Button - none could beat Massa's time.
Soon-to-be-McLaren driver Sergio Perez was up against a highly motivated Sauber team-mate in Kamui Kobayashi and had an off-track moment where his car scooped up a lot of gravel and bounced the floor heavily.
Then it was time for Sebastian Vettel to deliver a Suzuka masterclass and take over P1 with a 1:32.608 (the fastest lap on the harder tyre).
With six minutes of the session left to run Nico Hulkenberg's car was finally assembled and he went straight for the soft tyre, as did all the mid-grid teams in a bid for safety. These included Pastor Maldonado who put his Williams into P2.
With four minutes left of the session the drop zone was: 15.Vergne, 16.Ricciardo, 17.Kovalainen, 18.Petrov, 19.de la Rosa, 20.Glock, 21.Pic, 22.Karthikeyan 23.Schumacher (no time), 24.Hulkenberg (no time).
Late out of the pits (and facing a 10-place grid penalty for his Singapore misdemeanour, and hence reluctant to use a lot of tyres) was Michael Schumacher who was not taking the easy option by going onto softs, he had the harder tyre on.
Kimi Raikkonen proved how much quicker the softer tyre was by taking over P1 with a 1:32.221. He was soon displaced by Sergio Perez - who was still living dangerously at the Degna turns. Even Fernando Alonso (still behind Massa's time) was forced to use a set of softs to make himself safe. Then it was Kamui Kobayashi's time to send the crowd wild with a P1 time of 1:32.042.
All the drama was now at the back of the field with Schumacher's laps not being quick enough. He crossed the line to start his final flying lap with just seconds to spare and set off on a face-saving exercise.
While he was doing that Romain Grosjean leapfrogged to the top of the timesheets with a 1:31.029.
With Bruno Sennas team-mate easily getting into Q2 he was now under pressure to do likewise, lingering close to the dropzone with Jean-Eric Vergne. On his final lap he was clearly blocked by the Toro Rosso, something his engineer described as "unbelievable" and he couldn't improve. This left Schumi free at the very last second to climb forward to P16, allowing Vergne to go through in P17 and eliminate Senna in P18.
So out went: 18.Senna, 19.Kovalainen, 20.Glock, 21.de la Rosa, 22.Pic, 23.Petrov, 24.Karthikeyan
De la Rosa did particularly well to get ahead of a Marussia and a Caterham, but it was a poor result for Senna who needed to show now, more than ever, that he was capable fo retaining his seat for 2013.
It was straight onto soft tyres for everyone in Q2 with Kobayashi setting P1 at 1:32.368 before Sebastian Vettel set himself up to sit out the rest of the session with a 1:31.501
Massa went P2, Hamilton went P2, Button went P3 and then Mark Webber could only go P3.
Michael Schumacher chose to sit out much of the session but came out for the last dash to the flag. Running into the final four minutes of the session, the drop zone looked like: 7.Grosjean, 8.Alonso, 9.Kimi Raikkonen, 10.Perez, 11.Hulkenberg, 12.Maldonado, 13.Rosberg, 14.DiResta, 15.Ricciardo, 16.Vergne, 17.Schumacher.
Alonso finally got his lap together to take P3, Kimi Raikkonen could only manage P10, Paul diResta took P7, team-mate Nico Hulkenberg went one better with P6, Kamui Kobayashi grabbed P4 before Raikkonen made himself safe with P3.
Raikkonen's time had pushed Grosjean out of the top ten, but he was still on a quick one. Perez took P8 demoting Massa to P10 and DiResta to P11. Then, when Romain crossed the line in P7, it was Massa out too.
Felipe's final lap had been slower than his earlier time and the man who had looked like the fastest Ferrari fell behind Alonso yet again. So out went: 11.Massa, 12.DiResta, 13.Schumacher, 14.Maldonado, 15.Rosberg, 16.Ricciardo, 17.Vergne.
Michael Schumacher got the Mercedes bragging rights over Nico Rosberg and Paul DiResta lost out in the Force India team battle.
Qualifying 3Raikkonen was out early to set provisional pole at 1:32.208, but it was a big surprise that Lewis Hamilton couldn't beat that time on his first run coming immediately after the Finn on track.
Sebastian Vettel proved why he has been on pole at Suzuka at the three previous visits by putting in a provisional pole time of 1:30.839. Even at this stage it looked less 'provisional' and more like the 'actual' pole.
Jenson Button (facing a five-place gearbox penalty) stuck his McLaren into P2 before he was displaced by Mark Webber in P2. Webber's lap included a lock-up into the hairpin suggesting he could have gone quicker.
Alonso, Hulkenberg, Kobayashi and Perez stayed in the garage, suffering from a lack of soft tyres having used too many of them earlier.
Into the last two minutes and all ten cars were out on track (even though Hulkenberg failed to set a time). Perez grabbed P5 and then attention swung to Kimi Raikkonen who had gone off track at the Spoon corner bringing out the yellow flags. Despite the double waved yellows, Kamui Kobayashi was able to put his Sauber into P4 and Alonso ended up with P7.
Nobody else improved and the session ended with Vettel, now a four-times pole sitter at Suzuka, alongside team-mate Mark Webber on the front row. With serial claims of blocking by many drivers, existing penalties for Button, Schumacher and Hulkenberg, plus the Q3 yellow flags incident, the rest of the grid might take a lot of sorting out for tomorrow.
01. Sebastian Vettel Red Bull-Renault 1m30.839
02. Mark Webber Red Bull-Renault 1m31.090
03. Jenson Button McLaren-Mercedes 1m31.294
04. Kamui Kobayashi Sauber-Ferrari 1m31.700
05. Romain Grosjean Lotus-Renault 1m31.989
06. Sergio Perez Sauber-Ferrari 1m32.022
07. Fernando Alonso Ferrari 1m32.114
08. Kimi Raikkonen Lotus-Renault 1m32.208
09. Lewis Hamilton McLaren-Mercedes 1m32.327
10. Nico Hulkenberg Force India-Mercedes no time
11. Felipe Massa Ferrari 1m32.293
12. Paul di Resta Force India-Mercedes 1m32.327
13. Michael Schumacher Mercedes 1m32.469
14. Pastor Maldonado Williams-Renault 1m32.512
15. Nico Rosberg Mercedes 1m32.625
16. Daniel Ricciardo Toro Rosso-Ferrari 1m32.954
17. Jean-Eric Vergne Toro Rosso-Ferrari 1m33.368
18. Bruno Senna Williams-Renault 1m33.405
19. Heikki Kovalainen Caterham-Renault 1m34.657
20. Timo Glock Marussia-Cosworth 1m35.213
21. Pedro de la Rosa HRT-Cosworth 1m35.385
22. Charles Pic Marussia-Cosworth 1m35.429
23. Vitaly Petrov Caterham-Renault 1m35.432
24. Narain Karthikeyan HRT-Cosworth 1m36.734
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