The win was Johnson's third on the Nationwide Tour, but first since 2000. Sunday marked the fifth time this season that Johnson was in the final group in the final round, but this was the first he won.
'I've had a few close ones,' said Johnson, who pocketed $94,500 for the win and moved to fourth on the Nationwide Tour money list, thus earning him a spot on the PGA TOUR next year. 'This is great.'
The trio headed back to the par-5 18th at Empire Lakes Golf Course. All three had the length to reach in two and no one got in too much trouble off the tee.
It was the second shots that doomed Jones and Anderson. Both found the water with their approaches and Johnson took advantage. He knocked his second over the green near a grandstand, but was in command of the playoff.
Both Jones and Anderson took penalty drops and neither hit their fourth shots close to the flagstick. Johnson got a free drop and chipped inside two feet. He walked up, tapped in and hoisted the trophy.
Johnson shot a 4-under 67, while Jones and Anderson posted matching rounds of 5-under 66. The trio finished regulation at 11-under-par 273, one shot better than Tommy Tolles, who also managed a 66 on Sunday.
Johnson did not get off to the kind of start one would expect from the eventual champion. He double-bogeyed the first hole, but reclaimed both strokes thanks to birdies at five and eight.
At seven-under par for the championship, Johnson trailed several different leaders. It was his play on the back nine that got him the victory.
He birdied four in a row from the 13th hole to get to 11-under par. Johnson two-putted from close to 80 feet for par at 17, but did not give himself a great chance at birdie on 18.
It would not matter as Johnson walked off with the title a few minutes later.
'I got off to a bad start,' said Johnson. 'I got a few unlucky bounces. I made some putts and all of a sudden I was tied for the lead. I pulled it off the second time around.'
Overnight leader Tom Gillis only managed a 1-under 70 on Sunday and tied for fifth place with Brad Adamonis (66), Brian Smock (67) and Keoke Cotner (68). The group finished at 9-under 275.
Ricky Barnes (68), Jon Mills (68) and B.J. Staten (69) shared ninth place at minus-8.