He posted a 2-under 70 on Sunday and finished the tournament at 20-under-par 268. Mills carded a 3-under 69 to miss out on his chance to win.
McKenzie did get his first win on the tour and the $81,000 first-place check moves him into the top-20 on the money list. That assures him a spot on the PGA Tour next season.
'It hasn't really sunk in yet,' said the Australian. 'I've tried deliberately not to think about getting to the PGA Tour. It feels good to finally lock up my card.'
It came down to the wire as Mills took over the lead from McKenzie with three consecutive birdies from the seventh. Mills fell down the leaderboard with a double bogey at 14, but the pair were knotted when McKenzie bogeyed the 16th.
They both birdied the par-5 17th at the Cattail Course at Whirlwind Golf Club to stay at minus-19.
At the 450-yard, par-4 18th, both players had decent looks at birdie. Mills missed a 9-footer so the stage was set for McKenzie and the Australian rolled in a 5-footer to earn the win.
'It is nice to finally get it done,' said McKenzie. 'Standing over the putt, I knew I had put in all the practice. I was a little nervous. Now I can sit back and relax a little bit.'
Mills did not make enough birdies coming in, but was satisfied with the result.
'He birdied two coming in and I birdied one,' said Mills, who won the Canadian PGA Championship. 'We had a lot of fun out there. We had a good time and I'm happy with it.'
Jerry Smith fired a 6-under 66 and finished alone in third place at minus-17.
Camilo Villegas shot a 5-under 67 and tied for fourth place with Cameron Percy, who carded a 69 on Sunday. The pair was knotted at 15-under-par 273.
Charley Hoffman managed a 4-under 68 and came in sixth at minus-14. Craig Carmichael fired a 65 in the final round and tied for seventh place with Craig Bowden, who only mustered up an even-par 72. The pair came in at 13-under-par 275.