The Korean, who finished second alongside Rory McIlroy at last week's Korea Open, fired a closing 70 for a 3-under-par total that earned him an invitation to next year's Masters Tournament. He also secured a place in International Final Qualifying for The Open Championship along with runner-up Shohei Hasegawa of Japan, who shot a 71.
Hasegawa's compatriot Kenta Konishi (70) finished strongly to claim solo third place at 1-over.
After posting earlier rounds of 70, 72 and 69, Lee started the final day with a slender one-shot advantage over 16-year-old Dou Zecheng, who was looking to become the second Chinese player to win the championship after Guan Tianlang's victory in Bangkok 12 months ago.
After briefly drawing level with Lee at the second, a hole that Lee bogeyed, the bucket hat-wearing Dou (75) found birdies hard to come by as he struggled on the Garden Course's quick greens. He would finish in a tie for fourth with Australia's Lucas Herbert (68) and Lee Soo-min (70), also of Korea, six shots back.
Lee, 19, became the second Korean to win the championship after Han Chang-won claimed the inaugural event in 2009 at Mission Hills Golf Club in southern China.
He mixed two birdies and two bogeys over the front nine to turn in level-par 36. He pulled away from his challengers with a superb display of ball-striking that produced birdies at the 12th and 15th. A three-putt bogey at the last failed to take the shine off a dominant performance.
"Playing in the Masters has been my dream since I started playing golf," said the Seoul-born Lee, who won the Dongbu Promi Open on the professional Korean Tour last month. "I didn't think I would have an opportunity [to ever do so], so this is a great honor, as is playing in International Final Qualifying for The Open Championship. I have never been so excited."
Although Lee played like a seasoned pro down the final stretch, he did admit to not being able to shed his nerves until his tee shot at the par-3 17th, which he struck to the heart of the green.
"I have been looking at the leader board since the third round and I was a bit nervous," said Lee, who is likely to climb up the World Amateur Golf Ranking (WAGR) from his current position of 31 when the Ranking is updated on Wednesday. "I just tried to keep calm and it seemed to work. I knew I was going to win after the tee shot on the 17th hole.
"Everything worked well during the last two rounds ... I can't believe I am going to go to the Masters. I think I will only realize it tomorrow," he added.
While disappointed he couldn't make more inroads into Lee's lead, 20-year-old Hasegawa, who sunk a 15-footer for birdie on the demanding 18th to secure the championship's silver medal for finishing runner-up, said he was looking forward to competing at International Final Qualifying for The Open Championship.
"My putting let me down over the weekend, and I hope to return next year to get the trophy," said Hasegawa, who hails from Hiroshima. "But I'm very glad to have a chance to qualify for The Open. I think this is a great chance for my golfing career."
Although Guan, the defending champion, sparkled on day three with a 68, the 15-year-old, who received worldwide acclaim for his stunning performance at the Masters Tournament in April, wasn't at his best during the week. He failed to make a birdie during his final round of 73 to finish in a share of eighth alongside last year's runner-up, Pan Cheng-tsung of Chinese Taipei, Japan's Kazuya Koura and Brady Watt of Australia.
"It's been a pretty amazing year for me," said Guan, who holds the record for being the youngest player in history to play at the Masters. "I didn't defend my title this week, although I felt like my game was good, but I really appreciate the opportunities the tournament has given me."
Australia's Oliver Goss, who had already earned his spot in next year's Masters Tournament by virtue of his runner-up finish at the U.S. Amateur Championship, started the final round brightly by going out in 2-under 34. His hopes of making up further ground were derailed by a triple bogey at the 10th and a bogey at the 11th. Goss, who posted a 72, finished in seventh place with a 4-over-par total of 288.
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