The 18-year-old New Zealander, set to turn pro after the Masters, had a 17-under 271 total on The Vines Resorts composite course.
Japans Hiroyuki Fujita (67), Chiles Felipe Aguilar (68) and Englands Ross McGowan (70) tied for second in the event sanctioned by the European, Asian and Australasian tours. The second-place finishers all shared in the $298,000 that Lee would have collected if he was not an amateur.
Lee is the first amateur to win on the Australasian PGA Tour since Brett Rumford in the 1999 ANZ Players Championship at Royal Queensland. The last amateur winner of a European Tour event was Pablo Martin at the 2007 Portuguese Open.
Rarely showing emotion on the golf course, Lee pumped his arms briskly when a 15-footer on 17 went in for birdie. On 18, a hole he had birdied in the previous three rounds, his approach left him with about a 40-footer for eagle.
Lee twirled around in the air when long putt for a 3 lipped out and curled about a foot away. When he made his winning birdie putt, he again pumped his arms.
Lee will turn professional after the Masters in April and is setting his sights extremely high.
'I can't compare to Tiger Woods because he's one of the greatest players in the world and he's the No. 1 ranked player in the world.
'All I want to do is just break what he's done. Obviously I can't win three U.S. Amateurs in a row but I'll try to break his records on the PGA Tour,' said Lee.
Born in South Korea, Lee, who moved to New Zealand when he was 8.
American star Anthony Kim shot a 67 to tie for 25th at 10 under.
The final round came on Australias national day of mourning for the more than 200 people who died in bushfires around Melbourne on Feb. 7. Play was stopped early in the round for a minutes silence.