The 28-year-old Villegas went into the final round with a three-shot lead and he swiftly doubled that advantage by producing four birdies from the first 10 holes in unusually breezy and mild Floridian weather.
However Villegas, nicknamed 'Spider-Man' for the elastic-like flexibility he displays lining up putts, nearly lost his grip on the lead with three bogeys on the tougher back nine, including the 15th - the opener to the three hole 'Bear Trap' series.
But with his closest rival Kim bogeying the penultimate hole, Villegas regained his groove, avoiding trouble at the tricky 17th -- a par three over water -- and finishing his round in style with a 19-foot birdie putt.
"I had a couple of hiccups there in the back nine but winning golf tournaments is always tough. If there is a golf course where you can mess up coming in then it is this one, trust me. Those finishing holes are tough.
"I just picked my targets, put in good swings and took care of business," he added.
The Colombian finished 13-under-par for the week after carding a two-under on Sunday for his first PGA Tour win since his previous two in September 2008.
The wiry Villegas putted with confidence all week and gave himself a cushion for his back-nine wobble with a trio of excellent putts and a superb second shot from the rough on the challenging 10th.
Having driven into the trees to the right, the Colombian punched 200 yards out of the rough to land just five feet from the hole.
The victory crowned a demanding week for Villegas, who on Monday was in Bogota for a Pro-Am ahead of this week's Bogota Open, the first PGA sanctioned event in his native country and one that featured his younger brother Manuel.
"It's been a long week but man it's been a good one, I've loved every second of it," said Villegas at the end of his round.
"Today it was about coming here and taking care of business, I've done it all week but tournaments are about four rounds."
Villegas' victory sets him up perfectly for one of his favorite events of the year, the WGC-CA Championship at Doral near Miami next week.
The Colombian is a crowd favorite at the most Latin influenced event on the tour where he tied for fifth last year.
On Sunday, Kim was second on eight-under and Britain's Justin Rose equaled the course record with a six-under 64 to finish third at seven-under. Another Briton, Paul Casey tied for fourth place on six under with Fijian Vijay Singh.
Sam Saunders, the 22-year-old grandson of seven-times major winner Arnold Palmer, played on a sponsors exemption and finished tied for 17th.