The 30-year-old, in his third tournament back following a near-two year break to fulfil military duties, had tossed away the lead after his third bogey of the day at the par four 15th before his stunning finish sealed a first OneAsia Tour win.
"Amazing, I am so relieved," said Choi after signing for a final round of level par 72 and 10-under total.
"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."
His victory in the one billion Korean Won (588,925 pounds) event took him to the top of the OneAsia Order of Merit following the third of 10 tournaments on the calendar this year.
Choi, who had won three times on the domestic tour before his military break, held a one shot lead at the start of the day and eagled the fifth before he coughed up bogeys to keep the field in touch.
Lee, who fired a course-record 63 on Saturday, had his final round charge halted by a double bogey six on the 11th and could only par his way home as he settled for second place.
"This is my best result as a professional so I am very happy," the 21-year-old said after his nine-under total at Incheon's Sky 72 Ocean Course.
Australian Dimitrios Papadatos fired a timely final round of four-under 68 to finish in a tie for third with four others at eight-under.
(Writing by Patrick Johnston in Singapore; editing by Amlan Chakraborty)
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