Sebastian Vettel will start the Abu Dhabi title decider from pole position, with chief rivals Fernando Alonso third and Mark Webber only fifth.
The Red Bull drivers elected to do just one run in Q3, with the McLarens having already set times in the mid 1m39s a couple of minutes earlier.
Vettel immediately took provisional pole and then bettered his own time again, while Webber struggled to keep pace with his team-mate and remained behind the times the McLarens set on their first runs.
When the McLarens and Ferraris came back out for one lap at the end, Lewis Hamilton claimed a place on the front row alongside Vettel, seconds before Alonso pipped Jenson Button to the head of the second row.
Webber was left in fifth, and will start alongside Ferrari's Felipe Massa.
Hamilton had survived an earlier scare in Q2 when he was still to post a decent time in the final minutes of the segment. Having already out-braked himself to ruin an earlier lap, he was searching for a gap in the traffic when he appeared to delay Massa on the way into a left hander - though Hamilton did run off the track and collect a bollard in getting out of the way.
Button had complained of a "massive vibration" in his McLaren at the beginning of Q1, but after pitting for treatment to his brakes he found his pace, finishing second only to Vettel in Q2.
Mercedes bucked the trend as Michael Schumacher and Nico Rosberg did the majority of their running on the harder tyre. It worked for them in the early rounds, particularly Rosberg who was second in Q1 and third in Q2, but come Q3 they did only one run each and ended up with Schumacher eighth and Rosberg ninth.
Rubens Barrichello put Williams into seventh ahead of the two Mercedes, while Renault's Vitaly Petrov completed the top 10.
His team-mate, Robert Kubica ended his run of making it through to Q3 in every race at the final hurdle. Petrov had already made it through, and sat as high as seventh during Q2, but Kubica could not match his time and the Pole's scrappy last-gasp effort fell more than a tenth short.
Sauber's Kamui Kobayashi will start alongside Kubica in 11th, with Adrian Sutil (Force India) and Nick Heidfeld (Sauber) on row seven. Brazil pole-sitter Nico Hulkenberg was just 15th for Williams, with Vitantonio Liuzzi and Jaime Alguersuari concluding the Q2 runners.
The shame of joining the six new team drivers in the elimination zone at the end of Q1 was a battle between Toro Rosso team-mates Sebastien Buemi and Alguersuari.
Buemi held the spot going onto the final laps, but Alguersuari overhauled him by just over a tenth to make it into Q2.
At the back, Jarno Trulli out-qualified Lotus team-mate Heikki Kovalainen, with Timo Glock beating Lucas di Grassi and Bruno Senna ahead of Christian Klien.
Pos Driver Car Q1 Q2 Q3 1. Vettel Red Bull-Renault 1m40.318s 1m39.874s 1m39.394s 2. Hamilton McLaren-Mercedes 1m40.335s 1m40.119s 1m39.425s 3. Alonso Ferrari 1m40.170s 1m40.311s 1m39.792s 4. Button McLaren-Mercedes 1m40.877s 1m40.014s 1m39.823s 5. Webber Red Bull-Renault 1m40.690s 1m40.074s 1m39.925s 6. Massa Ferrari 1m40.942s 1m40.323s 1m40.202s 7. Barrichello Williams-Cosworth 1m40.904s 1m40.476s 1m40.203s 8. Schumacher Mercedes 1m41.222s 1m40.452s 1m40.516s 9. Rosberg Mercedes 1m40.231s 1m40.060s 1m40.589s 10. Petrov Renault 1m41.018s 1m40.658s 1m40.901s 11. Kubica Renault 1m41.336s 1m40.780s 12. Kobayashi Sauber-Ferrari 1m41.045s 1m40.783s 13. Sutil Force India-Ferrari 1m41.473s 1m40.914s 14. Heidfeld Sauber-Ferrari 1m41.409s 1m41.113s 15. Hulkenberg Williams-Cosworth 1m41.015s 1m41.418s 16. Liuzzi Force India-Ferrari 1m41.681s 1m41.642s 17. Alguersuari Toro Rosso-Ferrari 1m41.707s 1m41.738s 18. Buemi Toro Rosso-Ferrari 1m41.824s 19. Trulli Lotus-Cosworth 1m43.516s 20. Kovalainen Lotus-Cosworth 1m43.712s 21. Glock Virgin-Cosworth 1m44.095s 22. di Grassi Virgin-Cosworth 1m44.510s 23. Senna Hispania-Cosworth 1m45.085s 24. Klien Hispania-Cosworth 1m45.296s All timing unofficial