In Sunday's fourth round in Perth, the 18-year-old New Zealander shot 5-under-par 67, closing with birdies at 17 and 18.
His overall total, 17-under 271, beat Japan's Hiroyuki Fujita (67), Chile's Felipe Aguilar (68) and England's Ross McGowan (70), all of whom finished 16-under 272.
"My English is not 100 percent and I get really nervous when I'm doing the media stuff," Lee said in his post-tournament remarks. "It still feels like I'm in dreamland (and) hopefully no one wakes me up. I just kept saying to my caddy Jason, 'We can win this'!"
Lee also was the youngest-ever to win the U.S. Amateur Championship last summer after Spain's Pablo Martin, winner of the 2007 Portugal Open.
Because Lee is an amateur and ineligible for prize money, the runners-up received a larger portion of the tournament's purse.