Mills had matched course record with a 9-under-par 63 on Saturday, and his 54-hole score of 18-under 198 broke the tournament record by three strokes.
That put the 27-year-old in position for his first Nationwide Tour win, which he secured in style with just one bogey over his final 46 holes.
Ken Duke emerged as the only threat to Mills, but he finished alone in second place at 16-under-par 272 after shooting a 4-under 68 in the final round.
Nick Cassini and Erik Compton were one stroke further back at 14-under 274, while Kevin Johnson ended alone in fifth place at minus-12 after stumbling to a round of 2-over Sunday.
Mills fell to 17 under with a bogey at the par-4 fourth, snapping a streak of 31 holes without a bogey since he dropped a shot at No. 17 on Friday -- his eighth hole of the second round.
But after three consecutive pars, Mills dropped in a birdie at the par-3 eighth to get back to 18 under.
Johnson, who stood alone in second place after round three, birdied No. 1 to get to 15 under before dropping a pair of shots with bogeys at the par-3 fifth and the par-4 seventh.
That allowed Duke to emerge as Mills' closest challenger. Duke, who entered Sunday alone in third place at minus-12, collected three birdies on the front-nine to get to 15 under and added another birdie on No. 10 to pull within two of Mills.
That's where the two golfers stood heading into the second of two weather delays, which halted play from just after 3:00 until 4:30 p.m. ET.
When he returned to the course, Mills promptly birdied the par-5 12th to get to 19 under. Unable to keep pace, Duke parred No. 12 to fall three strokes off the lead with six holes to play.
Duke then stumbled to his first bogey of the day at the par-3 14th. That dropped him four strokes off the pace and all but sealed the win for Mills, who parred his final six holes while Duke collected one more birdie at No. 16.
Jerry Smith and Doug LaBelle II finished in a tie for sixth place at 11-under-par 277. Kenneth Staton, Carl Desjardins and Tom Scherrer ended one stroke further back to share eighth place.