Sebastian Vettel was given a helpful hand by McLaren on his way to his 12th pole position of the season, which he claimed in Japan
The Red Bull driver continued the team's domination of pole positions in 2011 with Jenson Button falling an agonising 0.009 short and Hamilton failing to get a final run after being overtaken on his outlap by Mark Webber and Michael Schumacher (via the grass) and missing the checkered flag.
Home favourite Kamui Kobayashi made it into the Top 10 to keep the Japanes efans happy.
It was bright autumn sun in Suzuka with an ambient temperature of 23C and the track up at 36C as Jarno Trulli's Lotus took to the track to kick off Q1. The first significant P1 time was set by Vitaly Petrov at 1:34.045. A very early running Sebastian Vettel then dislodged that with a 1:33.051 and Jenson Button - fastest in all three practice sessions - edged him out with a 1:33.018.
Fernando Alonso showed that Ferrari are far from out of it by taking P1 with a 1:32.817 which was quickest for the majority of the session. Many teams were being very careful about the high tyre degradation at Suzuka and running the minimum laps. Christian Horner of Red Bull thought there could be between three and five tyre stops during the race.
Running into the last five minutes, it was the new teams at the back of the grid. Tonio Liuzzi had been unable to get out because of a Cosworth engine failure and Nico Rosberg's Mercedes had suffered a hydraulics failure - so there was less pressure on the P18 slot. For the record it was 16.Kovalainen, 17.Barrichello, 18.Trulli.
The rest of the field weren't taking any chances and strapped on the soft Option tyres instead of the medium Prime tyre. It had a dramatic effect on the timesheets. All of a sudden Adrian Sutil put his Force India into P1 with a 1:32.761 and then Kamui Kobayashi sent the home fans into ecstasy by taking P1 with a 1:32.626.
With Rosberg not going out again, all the established teams were able to put on the faster tyre and pull themselves clear of the new teams, so out went:
18.Kovalainen, 19.Trulli, 20.D'Ambrosio, 21.Glock, 22.DiResta, 23.Rosberg, 24.Liuzzi
Jerome D'Ambrosio managed to beat team-mate Timo Glock's time at the very last moment (for a change), something Glock congratulated him for in the pits - which was nice to see. Rosberg was fairly sanguine about his place on the grid, but in a race with potentially five tyre stops - a lot can happen.
Adrian Sutil was out early in Q2 and set the benchmark time of 1:34.384. This was immediately put in context by Sebastian Vettel who reduced P1 to 1:31.424 on the soft tyres, followed home by Button in P2 and Webber in P3. But Lewis Hamilton looked in impressive form, taking P1 with a 1:31.139.
Sergio Perez had got his Sauber through Q1 but a hydraulics problem sidelined him in Q2 and he wouldn't take to the track. Perez (like Paul DiResta) had a bad case of flu and was struggling to speak.
With five minutes of the session left to run the danger positions were: 7.Schumacher, 8.Petrov, 9.Buemi, 10.Alguersuari, 11.Kobayashi, 12.Sutil, 13.Senna, 14.Barrichello, 15.Maldonado, 16.Di Resta (no time) 17.Perez (out of the car)
Maldonado put his Williams up to P9 early, but unlike other race weekends, there was no chance for multiple hot laps with the tyres good for one lap only. Kobayashi then sent the fans wild by jumping to P8. Adrian Sutil grabbed P9, Vitaly Petrov took P8 and Renault team-mate Bruno Senna moved up into P9 demoting Kamui san into P10.
But that was it, there were no other fast laps to be completed and Paul Di Resta had only managed P12. So out went: 11.Sutil, 12.DiResta, 13.Barrichello, 14.Maldonado, 15.Buemi, 16.Alguersuari, 17.Perez
The session that could have heralded an all-McLaren front row ultimately ended in disappointment for the Woking team. Kamui Kobayashi took to the track to put in a few sector times, and then return to the pits. He was saving tyres for the race and the battle with the two Renaults who would be in front of him.
On his first run Fernando Alonso ran too wide on the entrance to Spoon corner and opted out of the lap. Felipe Massa set provisional pole at 1:31.287 then Lewis Hamilton shattered that with a 1:30.617 - team-mate Jenson Button could only manage P2 and World Champion elect Sebastian Vettel was a couple of tenths back in P3.
So there were only five initial times: Hamilton, Button, Vettel, Webber, Massa and these looked all to have been set on used soft tyres. With precious little time left the cars came out for their second runs, this time on new soft tyres.
All the front-runners left the pits together and with little margin of error for missing the checkered flag at the end of the session. Vettel crossed the line to start his final lap followed by Button and then it should have been Hamilton, but instead it was Webber and Schumacher.
Camera replays showed that Hamilton had backed off from just behind Jenson Button but behind him, both Webber and Schumacher knew they were going to miss the line if they delayed. Webber passed Hamilton into the final chicane - Lewis sportingly giving him room - while on the outside Michael Schumacher's car took to the grass and re-emerged on the track in front of Hamilton.
As a result, neither Hamilton or Schumacher would get a final timed lap. Sebastian Vettel duly took P1 and Jenson Button came up 0.009 of a second short. Hamilton coasted to the pits but hung onto P3 while a great effort from Felipe Massa got him P4 ahead of Alonso and Mark Webber.
So yet again, another Red Bull pole, but with many tyre stops tomorrow, a lot of strategy to come. Renault proved that Singapore was just a blip in their season as they got both cars into the top 10. Petrov will be hoping for a much better getaway than he had last year, when he made contact with the barrier before Turn 1.
1. Sebastian Vettel Red Bull 01:30.466 14
2. Jenson Button McLaren 01:30.475 14
3. Lewis Hamilton McLaren 01:30.617 14
4. Felipe Massa Ferrari 01:30.804 15
5. Fernando Alonso Ferrari 01:30.886 13
6. Mark Webber Red Bull 01:31.156 14
7. Michael Schumacher Mercedes no time 10
8. Bruno Senna Lotus Renault no time 12
9. Vitaly Petrov Lotus Renault no time 17
10. Kamui Kobayashi Sauber no time 15
11. Adrian Sutil Force India 01:32.463 14
12. Paul di Resta Force India 01:32.746 10
13. Rubens Barrichello Williams 01:33.079 13
14. Pastor Maldonado Williams 01:33.224 14
15. Sebastien Buemi Toro Rosso 01:33.227 10
16. Jaime Alguersuari Toro Rosso 01:33.427 10
17. Sergio Perez Sauber 01:34.704 6
18. Heikki Kovalainen Team Lotus 01:35.454 3
19. Jarno Trulli Team Lotus 01:35.514 6
20. Jerome d' Ambrosio Virgin 01:36.439 8
21. Timo Glock Virgin 01:36.507 7
22. Daniel Ricciardo HRT 01:37.846 7
23. Nico Rosberg Mercedes no time 1
24. Vitantonio Liuzzi HRT no time 2