Day, 19, finished the event at 16-under-par 268.
The Australian also bested Andrew Johnson's 2005 scoring record of 270 at StoneWater Golf Club.
Scott Gardiner also carded a 67 to take second place at 15-under-par 269. Arjun Atwal fired a 5-under 66 to finish alone in third at minus-14. Joe Daley (70) was two strokes further back at 12-under-par 272.
Gardiner was in control most of the round, but two late bogeys cost him the title. He birdied the first and fifth to move to minus-13. Back-to-back birdies from the seventh gave Gardiner a two-stroke lead at 15-under.
Day, meanwhile, was cruising along. He picked up his first birdie at the fourth. He later birdied No. 11 to get back within one of Gardiner's lead. Gardiner pushed his lead back to two with a birdie on 13.
The big swing came at the par-4 15th, where Gardiner faltered to a bogey and Day carded a birdie for a two-stroke swing that created a tie for the lead at 15-under.
Gardiner dropped another stroke on 16 to fall one back. Playing one group ahead of Day, Gardiner birdied the last to get in a 15-under.
Day, who parred 16 and 17, responded with a birdie of his own at the last to claim the title.
David McKenzie, who shared the third-round lead with Day, closed with a 1-over 72 to slide into a share of fifth place at 11-under-par 273. He ended alongside Chad Collins, Martin Laird and John Riegger. Todd Fischer and Brock Mackenzie were one stroke further back at minus-10.