Scott carded a closing 70 at PGA National to finish nine under par, one shot ahead of playing partner Sergio Garcia, who was left to rue dropped shots on the 16th and 17th in his 71.
American duo Blayne Barber and Justin Thomas shared third place on five under, with Northern Ireland’s Graeme McDowell a shot further back in fifth after a closing 69.
Scott won the Masters in 2013 using a long putter and reached the top of the world rankings in May 2014, a week before his last victory in the Crowne Plaza Invitational, but has successfully reverted to a conventional club in order to comply with the ban on anchored strokes which came into effect on January 1.
The 35-year-old began the final round tied with Garcia and moved two shots clear with birdies on the first and fifth as he looked to become the first player since Phil Mickelson in 2009 to win on the PGA Tour after carding a quadruple bogey.
The Australian had enjoyed a three-shot lead before finding water twice on the par-three 15th in the third round to run up a seven, although a birdie on the 17th helped repair some of the damage.
Garcia had bogeyed the 17th before a birdie on the 18th took the good friends into the last day tied at the top of the leaderboard, but the Spaniard had to settle for nine straight pars on the front nine in the final round.
However, with Scott dropping a shot on the ninth after failing to get up and down from a greenside bunker and another on the 10th after a wayward drive, Garcia was back on level terms before missing from two feet for par on the 11th after his approach only cleared the water by a few yards.
Scott restored his two-shot lead after a superb approach from a fairway bunker on the 12th left him with a tap-in birdie, only for Garcia to reduce his deficit to a single shot with a birdie on the 14th.
Both players bogeyed the 16th and Garcia’s chances of victory effectively disappeared with another bogey on the next, although the Ryder Cup star at least birdied the last before Scott calmly tapped in for par to secure the win.
Speaking to Sky Sports after securing his 12th PGA Tour title, Scott said: ‘I’m so pleased. It’s been a long time between drinks on the PGA Tour, especially after I was in such good form the last time I won, but that’s the beauty of this game.
It felt like hard work out there to get it in the clubhouse and Sergio stuck with me the whole way and did not give me an inch. Fortunately it was enough to win.
‘The game was definitely there, although it was not as pinpoint as yesterday. It’s hard to do that two days in a row at PGA National but I hit some great shots at the right times and hit a lot of putts that hit edges today.’
Asked about reverting to the short putter, Scott added: ‘It was a tough change in some ways but I fully embraced it when I decided to make it at the Presidents Cup last year and I have enjoyed putting with the shorter putter since.
‘I feel like I am getting better and better and today was a great test. I made some and missed some. I’m going to try and get better next week and it’s certainly validated making the move to the short putter.’
Garcia was magnanimous in defeat, telling Sky Sports: ‘I think he deserved it. I am proud of the way I hung in there. I don’t feel like my swing was anywhere near where I wanted it to be but I scored nicely.
‘I putted well and chipped well but he played great. He played better than me at the end of the day, it’s as simple as that.’
Garcia, who had described his own play as ‘terrible’ after missing the cut in the Northern Trust Open, added: ‘There’s a lot of positive things from this week.
‘I fought hard, I stayed quite calm. It’s never easy but I gave it my all and unfortunately (hit) a couple of bad shots on a couple of holes and it was just not enough.’
Russell Knox, second and third in the same event over the past two years, finished joint-26th on two-over after following a brace of 70s to open with two 71s on the weekend.