The Englishman beat Vettel by 0.222 seconds to ensure that a Red Bull driver wasn't on pole for the first time this season.
Vettel has already claimed the World Drivers' Championship title for a second successive year but could not match Hamilton's lap of one minute 35.820 seconds at the Yeongam circuit.
"I'm very happy," said 2008 Championship winner Hamilton.
"I'm very proud of what the team has achieved over the last two races.
"It's one of the first positives I've had for a while. To be back on pole is a great feeling. I've had some difficult races in the past and we'll try and redeem ourselves tomorrow."