Villegas overcame a five-shot deficit by making six birdies over his last 11 holes for a 4-under 66, then beat Garcia with a par on the 233-yard 18th hole used in the playoff.
The 26-year-old Colombian, who had gone 85 starts on the PGA Tour without winning, picked up his second in a row with a finish that brought the gallery to life on a sunny afternoon at East Lake.
He birdied the 17th hole from 12 feet to catch Garcia, then twice hit beautiful lag putts from outside 45 feet, once in regulation to finish at 7-under 273, then in the playoff to cap off his season in style.
Villegas, who will move to No. 6 in the world rankings, earned $1.26 million for winning the Tour Championship.
I cannot emphasize how hard Ive worked, Villegas said.
Anthony Kim and Phil Mickelson each shot 69, and each had a chance to join the playoff. Kim, playing in the second-to-last group with Villegas, missed from 30 feet. Mickelsons 20-foot birdie putt stayed above the hole.
Garcia missed a 20-foot birdie putt to win, then never gave himself much of a chance on the 18th hole in the playoff. He came out of the shot, and it wound up in deep rough some 30 yards short and right of the flag. His chip stayed in the collar of the green, and a chip to extend the playoff was well short.
It was the third consecutive time Garcia has blown a 54-hole lead on the PGA Tour over the last three years, including a six-shot advantage at the Wachovia Championship in 2005 and a three-shot lead in the 2007 British Open at Carnoustie.
I doubted myself too much early on, and it cost me, he said.
The consolation prize might be the Vardon Trophy for lowest adjusted scoring average. Garcia came into the Tour Championship trailing Mickelson by one-hundredth of a point, and wound up at 69.40. Mickelson finished at 69.42.
Tiger Woods, who had season-ending knee surgery after winning the U.S. Open, did not play the required 60 rounds to be eligible for the award, which will not be official until the Tours Fall Series ends the first week of November.
Fun way to finish the year, have it come down to the last shot, Mickelson said.
What was supposed to be the highlight of the Tour Championship ' the FedEx Cup ' turned into an afterthought. Vijay Singh effectively wrapped up the $10 million prize two weeks ago in St. Louis, so all he had to do was finish 72 holes at East Lake and sign for the correct score to win the FedEx Cup.
I made one birdie and one bogey. It was easy not to make a mistake, he said.
Singh closed with a 70 and tied for 22nd in the 30-man field, but none of that mattered. He won the first two playoff events to take the drama out of the FedEx Cup for the second consecutive year.
Villegas missed the cut at The Barclays in the first round of the playoffs, which ultimately cost him. He wound up 551 points behind in the FedEx Cup, but that was only bookkeeping.
While the FedEx Cup suffered another dull finish, the Tour Championship was anything but that. Over the back nine, it turned out to be one of the best regular PGA Tour events of the year.
Mickelson, Garcia, Kim and Villegas ' four of the hottest commodities on a tour without Woods ' had at least a share of the lead along the back nine at East Lake. They were in the final two groups. At least one player made birdie or bogey on every hole except the 18th, which yielded only one birdie in the final round.
Villegas might have been the one player no one expected to be there.
He started the final round five shots out of the lead, and despite a pair of birdies, gave it all back and more with a tee shot into the water on the par-3 sixth, and a bogey on the next hole. But the Colombian showed his flair, storming right back into contention with three straight birdies as the leaders faltered.
Garcia, also a playoff loser to Singh in The Barclays, failed to birdie the par-5 ninth from a greenside bunker, and didnt make his first birdie until the 12th hole. Mickelson was reminded how much his putter has held him back, missing several chances inside 12 feet.
Kim was the most steady of the bunch, but after taking the outright lead with a 20-foot birdie on the 11th hole, the 23-year-old did not make another birdie the rest of the round.
Kim was the only player who failed to birdie the uphill, par-5 15th, as the others shared the lead at 7 under. Mickelson and Villegas both dropped shots on the 16th by missing the green and hitting chips outside 10 feet, but Villegas redeemed himself.
From the first cut of rough on the right side of the 17th fairway, he made an aggressive swing, knelt and clasped his hands as if praying while watching his ball head left of the flag. It caught enough of the green to settle 12 feet away, and he made it for birdie.
Garcia went from a three-shot lead to a two-shot deficit until an 18-foot birdie on the 12th got him back in the game. He was solid the rest of the way until the playoff.