The Spaniard was beaten by team-mate Felipe Massa for the fifth time in six races and the eighth occasion in 17 grands prix this season.
The Brazilian was eighth quickest in the top 10 shoot-out, behind Raikkonen, who has been allowed to start from the back after his car failed a front-floor deflection test, Sauber's Nico Hulkenberg and Lotus's Romain Grosjean.
McLaren's Sergio Perez and Toro Rosso's Daniel Ricciardo completed the top 10, while Force India's Paul Di Resta was 12th, just behind Alonso.
Ferrari have been struggling with a lack of traction but Alonso was 0.104secs adrift of Massa in second qualifying, doing little to quieten questions about his form in qualifying in the second half of this season.
His erstwhile title rival Vettel will be just as disappointed with second place.
The 26-year-old was fastest after the first laps in the top 10 shoot-out but after Webber pipped him on the Australian's final run, Vettel failed to improve.
Vettel flicked his head in frustration several times as he crossed the line after completing his final lap.
Webber said: "This weekend has gone pretty smoothly. Not the smoothest path to the start of Q2 or Q1, we were not electric. We changed the car quite a bit and I got more and more comfortable as the session went on. It made me more comfortable in the final sector, where Seb has been quick, so I was able to match him there and keep where I had been quick already."
Vettel said he made a mistake in Turn One. "I was pushing hard, that's the reason behind it," he said. "You can always say there is a bit here and there, but if you push to the maximum and try to get everything out you can do mistakes.
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"I'm not very proud of that. But I did what I could and it wasn't enough to be on pole. Mark deserves to be on pole."
Red Bull were in a league of their own, half a second clear of Rosberg, but Hamilton lost any chance of a front-row start when he got on to the kerb on the exit of Turn 13 and then spun at Turn 14 on his final lap.
Hamilton said over the radio that he felt something had broken on the car and the team later discovered that the right rear suspension wishbone had broken.
Team principal Ross Brawn said: "It's a fast left-hander and he got the car fully on the kerb. We need to analyse what happened because it's a part we have run all year, but I don't think there are any risks for the race."
Hamilton was half a second up on his previous best lap when the incident happened, with his favourite sector three to come. He ended qualifying 0.544secs off Webber's pole time.
Hamilton said he was hopeful he could compete with the Red Bulls for his first victory since the Hungarian Grand Prix at the end of July.
"The car has been feeling great this weekend," he said. "We have closed the gap a little bit. I don't know why all of a sudden they have come back so far. I think we have a good chance to fight for a win."
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