Choi, the World Number 45, was one ahead of 329th-ranked Richard Johnson overnight, but it was the Swede who struck first in their third round duel.
He made a five foot birdie putt on the short fourth after Choi had three-putted it, but on the very next hole the two shot swing was in the other direction. Choi made a 25 footer and Johnson, twice in the left-hand rough, failed to get up and down.
When both two-putted the long ninth for birdies they were ten under and nine under respectively, with Open Championship winner Louis Oosthuizen one stroke further back in third.
The 27 year old South African, trying to become the first player to win The Open Championship and then take another European Tour title seven days later, three-putted from a mere 12 feet for a bogey six at the ninth, but birdied the next from further out.
Italian Edoardo Molinari, for whom a top two finish would elevate him into the all-important top nine on Europe's Ryder Cup table, turned at seven under, but fell five off the pace by starting the back nine with back-to-back bogeys.
Northern Ireland's Michael Hoey, meanwhile, also climbed to seven under, but hooked his approach to the 430 yard tenth into the water.
The former British Amateur Champion, who had his first European Tour victory in Portugal last year, double-bogeyed there, birdied the short next, but then three-putted for a six on the 548 yard 12th to be five under.
Both Choi and Johnson bogeyed the tenth, but the Asian golfer, twice five clear during the second round, opened a two shot lead when he pitched to six feet on the long 12th and made the birdie putt.
The dog-leg 581 yard 13th was always likely to prove some drama as rain started and so it proved.
Oosthuizen drove in the water, but hit a superb third to 15 feet and made the birdie putt to close the gap to one again.
Then Choi was incredibly lucky, his approach stopping on the edge of the lake. He took off his shoes and socks, waded in, splashed the ball out and over the green, but got down in two for a par that kept him ahead.
Johnson matched Oosthuizen's birdie, though, and was also only one back.
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