The Australian stormed to pole on the last lap of qualifying, finishing 0.074 seconds ahead of Vettel. Hamilton was third followed by championship leader Fernando Alonso of Ferrari.
Lotus' Kimi Raikkonen qualified fifth, meaning the top five in the Formula One standings fill the top five grid slots, raising the prospects of a vital shootout Sunday.
"I was happy with my lap there, it was solid and it's good to get pole," Webber said. "It's a great place to start the race from. I'm looking to get off the first corner very well, that's important as there are two long straights after that."
Vettel has won the past two races, in Singapore and Japan, and would overtake Alonso in the standings with a third consecutive win Sunday. The German dominated the practice sessions and topped the times in the first two sessions of qualifying, but when it mattered, he could not match the time set by his teammate.
"On the last run, I had to back off starting the lap as (Felipe) Massa was there, it wasn't his fault, but I had to back off," Vettel said. "Nevertheless, the second lap in Q3 wasn't good enough."
Webber, who recorded only his second pole of the season after Monaco, improved his lap time by a half-second on his final run.
Vettel can take some comfort in the fact that neither pole-sitter in the first two editions of the Korean Grand Prix had gone on to win on Sunday.
It was an encouraging result for Hamilton, who almost failed to advance to the second session of qualifying, making it through by just a quarter-second. The Briton said he expects it will be a challenge to overtake the Red Bulls on Sunday.
"It will be very tough to get ahead of them but we've put ourselves in as good a position as we could," Hamilton said. "It was very tough this weekend. These guys have clearly made quite a big step within the last two races so we've just got to keep pushing."
McLaren driver Jenson Button made an error and then was forced to slow for a late yellow flag in the second qualifying session and finished a disappointing 11th.
Raikkonen, who is third in the standings despite not having won a race in his comeback season, qualified fifth, ahead of Ferrari's Felipe Massa.