Webber was just 0.227secs ahead of Hamilton, with the Englishman heading Alonso by only 0.065secs.
Webber said: "Most qualifying sessions have been very tight and I'm very happy to get the job done today. It was a reasonable lap and we did it when it counted. Tomorrow is the main day and I'm in a good position to get a good result."
Hamilton said: "It's going to be very tough to get ahead of them but we have put ourselves in as good a position as I could. We're not that far off. Race pace looked quite good yesterday and I'm just happy to have had a good lap."
Korean Grand Prix: Mark Webber's pole lap
McLaren team boss Martin Whitmarsh added: "Mark put in an excellent lap in the end. I'm not sure we expected him to pull that one out. Sebastian, Lewis and Fernando all queued behind Mark will make it quite exciting, I'm sure."
Ferrari team boss Stefano Domenicali said: "We are never pleased because we would like it to be the other way around but if you remember where we were in qualy in terms of gap in [the previous races at] Singapore and Suzuka that means we have made another step in the right direction.
"The target was to start on the second or third row and that has been achieved so we need to have a good race tomorrow. On Friday the race pace was not bad so let's hope to have a clean start."
Alonso has retired at the start in two of the last four races.
Button made a mistake on his first run in second qualifying, locking a front wheel and then could not improve on his final lap because he had to slow for caution flags waved for the broken down Toro Rosso of Daniel Ricciardo.
Australian Ricciardo has since been handed a five-place grid penalty for changing his gearbox.
Mercedes were fined 10,000 Euros for the unsafe release of Michael Schumacher from his pit garage after the German pulled in front of Lewis Hamilton during Q3, forcing the McLaren driver to run off the pitlane and drive around the seven-time world champion.
Korean Grand Prix 2012, day two
Saturday, 13 October: Qualifying replay 13:00 BBC One.
Korean Grand Prix 2012, day three
Sunday, 14 October: Race 07:00 BST; BBC One (from 06:00), online and BBC Radio 5 live (from 06:55). Race replay 14:05 BST; BBC One. Highlights 19:00 BST BBC Three.
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