Consecutive 7-under 65s saw her finish on 21-under at the Robert Trent Jones Golf Trail's Magnolia Grove complex and earn a one-stroke victory over Jessica Korda and Pornanong Phatlum.
The 21-year-old Californian - who shot 67 and 70 in the first two rounds - had only one previous top-10 finish to her name, an eighth-place at the 2011 Navistar LPGA Classic, also in Alabama.
"I'm a little shocked," Johnson said. "I didn't even realise I shot 65. The whole back nine, I don't know what was happening.
"The birdie putt on 17, that's when I started thinking a little more about winning the tournament. A little bit on the front nine, but you can't afford to think about that."
Johnson, who birdied four of the final six holes, changed to a putter which she says looks like a spaceship after missing the cut at the Kingsmill Championship earlier this year.
"I hit the ball really well. It was like when I missed the cut I felt like I should be playing," she said. "And I went and saw my coach right away in Florida and worked some things out, I put the spaceship putter in the bag and now the putts are going in.
Defending champion Stacy Lewis played with Johnson and said what was happening did not really register with her.
"It was fun there at the end, because Jennifer was making putts and I don't think she realised what she was doing," she said.
"I told her when I hugged her, 'I think you just won yourself a golf tournament.' And she's kind of like, 'What?' It was really cute."
Korda shot 68 while Phatlum ran Johnson close with a 63.
Two strokes behind the winner were Karrie Webb (68), third-round leader Chella Choi (70), Anna Nordqvist (69), Jiyai Shin (63) and Ariya Jutanugarn (65).
- Sports & Recreation
- Jessica Korda
- Pornanong Phatlum
- Robert Trent Jones Golf Trail