SEOUL, 24 May 2015 (AFP) - Choi, who had led the field after every round, closed with a par 72 round to finish the tournament in Incheon on 10 under.
The 21-year-old Lee, who broke the course record on Saturday with a barnstorming round of 63, managed a 71 in the final round, to leave him nine-under overall.
Australian Dimitrios Papadatos (68), New Zealander Gareth Paddison (69) and Koreans KT Kim (70), Wang Jeung-Hun (73) and Park Jae-Bum (70) were tied for third two shots behind the winner.
It was a welcome win for Choi who was playing in only his third tournament back on tour since finishing a 20-month stretch of military service, which is mandatory for every able-bodied South Korean male between the ages of 18 and 35.
"Amazing, I am so relieved," the 30-year-old said.
"It was a difficult battle all the way and I am very pleased my game held up. It is an emotional victory considering everything and a surprise to come so soon. I guess I was just very up for it," he said
Choi had a one-shot lead at the start of the day, but at the turn he and Lee were tied in front on 11 under.
However, Lee made a costly double bogey on 11 to leave Choi two ahead.
Choi then faltered with bogeys at the 12th and 15th, but rallied at the last to sink the long, pressure putt and secure the title.
Leading final round scores: (South Korean unless stated)
278 - Choi Jin-Ho 68-68-70-72.
279 - Lee Soo-Min 73-72-63-71.
280 - Dimitrios Papadatos (AUS) 74-69-69-68, Gareth Paddison (NZL) 70-73-68-69, Park Jae-Bum 72-69-69-70, Kim Kyung-Tae 73-69-68-70, Wang Jeung-Hun 70-74-63-73.
281 - Park Sang-Hyun 68-75-70-68, Kim Seung-Hyuk 74-68-67-72, Kang Sung-Hoon 69-69-69-74.