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It was Webber's third straight pole as the overall Formula One leader goes for a third consecutive race victory. Red Bull has taken pole in all seven races this season.
Webber set a new qualifying record with a lap of 1 minute, 26.295 seconds around the Istanbul Park Circuit to lead Hamilton by less than two-tenths of a second.
Sebastian Vettel starts third after locking up his Red Bull during his final flying lap. Defending champion Jenson Button of McLaren completes the second row.
Fernando Alonso, Red Bull's closest competitor in the drivers' standings, starts 12th for Ferrari.
First since 2001
Red Bull is the first team to secure seven straight poles since Ferrari did so in 2000-'01. Four of the five winners at the "Otodrom" started first on the grid.
"It hasn't been the smoothest of weekends for us in getting the running in," said the 33-year-old Webber, who also had a new engine put into his car after Friday's practice. "I was a little bit on the backfoot going in to be honest. But I dug in and got the best out of it."
Hamilton, with girlfriend and pop singer Nicole Scherzinger watching on, put himself in the running for a first victory of the season.
"It's a real boost for me and my team knowing we have a very good baseline pace and our race pace is even better," Hamilton, the 2008 world champion, said after overcoming a spinout at turn 8 in morning practice.
Michael Schumacher's qualifying session also finished at the high-speed corner as the Mercedes driver went off into the gravel.
He had already set the fifth best time to sit ahead of teammate Nico Rosberg. Renault's Robert Kubica starts seventh ahead of Felipe Massa, who leads Ferrari going into its 800th GP.
Red Bull v McLaren
Webber and Hamilton ran untroubled flying laps to take the first two slots for Sunday's 58-lap race while their teammates couldn't get their last laps together.
Vettel's brakes cost him a chance to catch his teammate while Button pulled off into the pit lane before completing his lap.
"It's a bit frustrating," said Vettel, who was running smoothly in the first two sessions. "When it counted today it didn't all come together and we need to see why."
Vettel has been plagued by technical problems over the past races, while Webber has soared with a perfect car. They both have 78 points but Webber leads the championship thanks to his two wins.
On Saturday, Vettel was left shaking his head after the team released Webber ahead of him for the last lap.
"We're quite lucky not to be fourth, it was only a few hundredths of a second," Vettel said.
Vettel and Button weren't the only disappointed drivers. Alonso locked up his brakes on his penultimate lap of the second qualifying session, and then had a poor finish on his last lap to miss out on the final session.
That means the Spanish driver has plenty of positions to make up for a second straight race after starting last in Monaco to eventually finish sixth.
Alonso has 75 points, Button has 70, Massa - a three-time winner here - has 61, Hamilton and Kubica share 59 and Rosberg has 56. Renault's Vitaly Petrov starts ninth ahead of Kamui Kobayashi, who will be looking to earn Sauber its first points of the season.
Qualifying result from the Turkish Grand Prix in Istanbul on Saturday
1. Mark Webber (Australia) RedBull - Renault 1:26.295
2. Lewis Hamilton (Britain) McLaren 1:26.433
3. Sebastian Vettel (Germany) RedBull - Renault 1:26.760
4. Jenson Button (Britain) McLaren 1:26.781
5. Michael Schumacher (Germany) Mercedes 1:26.857
6. Nico Rosberg (Germany) Mercedes 1:26.952
7. Robert Kubica (Poland) Renault 1:27.039
8. Felipe Massa (Brazil) Ferrari 1:27.082
9. Vitaly Petrov (Russia) Renault 1:27.430
10. Kamui Kobayashi (Japan) BMW Sauber - Ferrari 1:28.122
11. Adrian Sutil (Germany) Force India-Mercedes 1:27.525
12. Fernando Alonso (Spain) Ferrari 1:27.612
13. Pedro de la Rosa (Spain) BMW Sauber - Ferrari 1:27.879
14. Sebastien Buemi (Switzerland) Toro Rosso - Ferrari 1:28.273
15. Rubens Barrichello (Brazil) Williams - Cosworth 1:28.392
16. Jaime Alguersuari (Spain) Toro Rosso - Ferrari 1:28.540
17. Nico Huelkenberg (Germany) Williams - Cosworth 1:28.841
18. Vitantonio Liuzzi (Italy) Force India-Mercedes 1:28.958
19. Jarno Trulli (Italy) Lotus - Cosworth 1:30.237
20. Heikki Kovalainen (Finland) Lotus - Cosworth 1:30.519
21. Timo Glock (Germany) Virgin - Cosworth 1:30.744
22. Bruno Senna (Brazil) HRT - Cosworth 1:31.266
23. Lucas Di Grassi (Brazil) Virgin - Cosworth 1:31.989
24. Karun Chandhok (India) HRT - Cosworth 1:32.060