Webber drops back from third to 13th as automatic punishment for picking up his third reprimand of the season for accepting a lift back to the pits from Alonso in what stewards considered a dangerous manner at the last race in Singapore.
Vettel's pole was his sixth of the season - more than anyone else - and had looked locked on after an impressive performance in Saturday's final practice session.
Vettel's time came on his first run in the final part of qualifying. He went out again at the end of the session but aborted his lap when he was held up by Raikkonen in the last few corners.
"It was fairly close," Vettel said. "As expected, Mercedes was pretty strong, so it was a tight battle.
Top three drivers on Korean qualifying
"Bit of a surprise this year we are very good in sector one, which is mainly straights and slow corners. That's good - it's the easiest place to make up time in the race. We improved the car - I wasn't that happy after Friday; that's why I was happy after qualifying."
Hamilton added: "We did as good a job as we could. I feel I got the most out of the car. In general it's been a good weekend and I really hope tomorrow we're able to fight with them."
Webber's penalty also drops him back behind Ferrari's Felipe Massa, who qualified sixth fastest, Sauber's Nico Hulkenberg and Esteban Gutierrez, Lotus's Kimi Raikkonen, the McLarens of Sergio Perez and Jenson Button and Daniel Ricciardo's Toro Rosso.
Webber said: "We had to take a bit of pace out of the car for qually. Not much, but just looking at how we would compromise the car for qually looking to the race. It was a good little battle. I'm well and truly out of position but we'll fight and come back through."
Scot Paul Di Resta starts 15th in his Force India, one place and 0.287secs behind team-mate Adrian Sutil.
Marussia's Jules Bianchi was handed a three-place grid penalty and a reprimand for impeding Di Resta and will start last.
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