Johnson's winning total of 20-under-par 264 shattered the old scoring record. Chris Couch set the old mark of 270 in 2003.
With the win and the $139,500 first-place check, Johnson overtook Roland Thatcher for the top spot on the money list.
'It's nice. I didn't come in here with any goals of getting into the No. 1 spot,' admitted Johnson. 'I figured I had to win and Roland had to fall off a little bit there. I just had a fun week.'
Michael Letzig, who triple-bogeyed the 18th on Saturday, fought back with a 5-under 66 to end alone in second place at 19-under-par 265. He also moved to 12th on the money list as the top 25 gained their PGA TOUR cards for next season.
Tom Scherrer and Martin Laird shared third place at minus-18. Scherrer jumped from 27th to 20th on the money list to earn his PGA TOUR card.
Brenden Pappas and Scott Gardiner were one stroke further back at 17-under-par 267. Pappas, who was 25th on the money list for the last four weeks, climbed to 22nd and will compete on the PGA TOUR next year.
'I was so nervous out there today,' admitted Pappas. 'I took probably two minutes on every shot the last three holes just trying to compose myself. I was trying to get to a place where I was relaxed and could perform'
Johnson got off to a flying start with an eagle on the par-5 opening hole. He came right back with a birdie on the second and another on the fourth to get to 20-under.
The Welshman stumbled to his first bogey on the par-3 seventh. He parred five straight from there.
Johnson moved back to 20 under with a birdie on the par-5 13th at Barona Creek Golf Club. He picked up another birdie on 17 to pad his lead. Johnson did close with a bogey, but that only cut his winning margin from two to one.
'I got off to a flyer today. I guess I was five ahead at one point and I started wondering if I could blow this one,' joked Johnson, who won for the fourth time on the Nationwide Tour.
Letzig, who was in control of the tournament until Saturday's 18th hole, also got off to a hot start. He birdied three of the first five holes to move to minus-17.
The 27-year-old Letzig stumbled to his only bogey on the par-3 seventh. He parred the next two and trailed by three around the turn.
Letzig dropped in back-to-back birdie putts from the 13th to get within one. Johnson created room with his birdies on 13 and 17, but Letzig closed the gap with a birdie on 17.
'That was very gratifying. I made a mess of this hole (Saturday) and man I had a hard time letting it go,' said Letzig of the 18th hole. 'It was really, really good to come out and get off to a great start like I did.'
David Hearn fired a 7-under 65 to take seventh at 16-under-par 268. Kelly Grunewald, Garth Mulroy, B.J. Staten and James Driscoll shared eighth at minus-15.
The top 25 on the money list finished like this: Johnson, Thatcher, three- time winner this year Nick Flanagan, Jon Mills, Jason Day, Nicholas Thompson, Matthew Jones, Justin Bolli, Patrick Sheehan, Paul Claxton, Ron Whittaker, Letzig, Laird, Kyle Thompson, Omar Uresti, Marc Turnesa, Brad Elder, Chez Reavie, John Riegger, Tom Scherrer, Scott Sterling, Pappas, Chad Collins, Driscoll and Jimmy Walker.