American Lewis shot a 71 to finish on 15-under for the tournament, with Choi - who had joined the second-round leader at the top of the leaderboard after round three - only managing a 72.
Paula Creamer, who suffered whiplash injuries in a road accident on her way to the airport in Thailand last Sunday, managed to finish third - just two shots behind the winner.
Fourth was Thai teenager Ariya Jutanugarn, who spectacularly threw away the Honda Thailand LPGA when leading by two strokes with one to play last weekend.
Lewis was especially proud of an eagle on the seventh after hitting a hybrid to the green of the 493-yard hole.
"That hybrid was probably the best shot I've ever hit," said the 28-year-old. "I held it up against the wind just perfectly."
That took her a shot ahead of Choi and two clear of Paula Creamer, a lead she consolidated in the following holes.
However there were worrying moments for her on the back nine: she found the water on the 15th then put the ball into a bunker on the short 17th to lead Choi by only a stroke - and Creamer by two - ahead of the par-five 18th.
Unlike her rivals, she reached the green in two, which took the pressure off; however she three-putted to allow Choi a birdie chance to force a play-off.
"I played with Na Yeon for three days and she made putt after putt after putt. I fully expected her ball to go in," said Lewis.
It narrowly missed to give Lewis her sixth title on the LPGA Tour and put her third in the world behind Yani Tseng and Choi.
"Ultimately I'd like to get to No.1 - and wins are the way to get there," she added.
Tseng was tied for 28th on two-under while American defending champion Angela Stanford was 56th in a finishing field of only 60.
Taiwanese-American Candie Kung and Americans Danielle Kang and Jessica Korda finished on nine-under, tied for fifth.
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