NASSAU, Bahamas, May 26, 2013 (AFP) - After a bogey-free final round, Lee finished on 11-under 126 for 36 holes played in three 12-hole rounds due to course flooding.
She foiling American Cho's bid for her first LPGA triumph after a seven-under 40 in the final round.
Until a third-place finish earlier this month at the Kingsmill Championship, Lee's best LPGA showing was a share of fourth at last year's US Women's Open.
"I can't believe it," Lee said.
Severe winds and rain nagged players over the last round, which was needed to reach the minimum 36 holes that made the tournament official.
"It was tough to play," Lee said. "It was blowing hard. And rain too. It was tough."
LPGA officials came up with the 12-hole, three-day format to salvage what had been planned as a 72-hole event. The course was flooded Tuesday by a severe storm that dropped more than a foot of rain, dooming hopes of playing Thursday.
The par-3 fourth hole was dropped Sunday in favor of the once-flooded par-5 18th, changing the layout from a par-45 to a par-47 makeshift layout using six holes from each of the Ocean Club's front and back nines.
Lee, 24, opened with three birdies in a row and added another at the eighth, a tap-in birdie, to reach 10-under for a one-stroke lead over Cho with four holes to play.
Lee endured long waits before her tee shot and approach at the oceanside penultimate hole before leaving a long birdie putt four feet short, but she dropped the tension-packed putt to stay ahead.
Blasting her second shot onto the green at the par-5 final hole just before a heavy rain began, Lee missed an 18-foot eagle putt but tapped in for birdie and the win, which came only when the last group finished to make it official.
Cho opened with a birdie, added another on the par-5 third hole and then eagled the par-5 fifth hole with a stunning approach from the fairway.
Back-to-back birdies at the eighth and par-3 ninth, the latter from 15 feet, and another at the par-5 12th, the course's usual last hole, put Cho in the clubhouse with the best finish of her career.
"I have no idea (how I played so well)," Cho said. "I was just one shot at a time."
Cho, whose career best had been a share of sixth at the 2008 LPGA Championship, finished in the money for only the third time this season.
Sweden's Anna Nordqvist was third on 129 with a group sharing fourth on 130 including Japan's Mika Miyazato, France's Karine Icher and Americans Mindy Kim, Paula Creamer and Cristie Kerr.
Leading scores Sunday after the final round of the Pure Silk Bahamas LPGA Classic (USA unless noted, 12-hole rounds with par-45 first and second rounds, par-47 last round due to course flooding):
126 - Lee Il-Hee (KOR) 41-43-42
128 - Irene Cho 45-43-40
129 - Anna Nordqvist (SWE) 40-44-45
130 - Karine Icher (FRA) 41-44-45, Mindy Kim 39-46-45, Paula Creamer 43-42-45, Cristie Kerr 44-40-46, Mika Miyazato (JPN) 42-43-45
131 - Giulia Sergas (ITA) 46-42-43, Katie Futcher 42-43-46, Heather Bowie Young 39-45-47, Julieta Granada (PAR) 41-42-48
132 - Alena Sharp (CAN) 41-50-41, Jennifer Rosales (PHI) 46-43-43, Caroline Masson (GER) 45-43-44, Jennifer Johnson 42-46-44, Ryu So-Yeon (KOR) 42-46-44, Brittany Lang 41-46-45, Sandra Gal (GER) 44-43-45, Natalie Gulbis 45-42-45, Ai Miyazato (JPN) 43-43-46, Yoo Sun-Young (KOR) 42-44-46, Lexi Thompson (USA) 45-41-46, Morgan Pressel 43-42-47, Lindsey Wright (AUS) 44-38-50, Paola Moreno (COL) 40-41-51
133 - I.K. Kim (KOR) 44-45-44, Caroline Hedwall (SWE) 44-42-47, Stacy Lewis 44-42-47, Mina Harigae 42-42-49, Park Hee-Young (KOR) 41-43-49