Villegas closed with a 2-under 68 for a two-shot victory over Dudley Hart, whose birdies on the final two holes earned him a spot in the Masters.
With one playoff event remaining, the FedEx Cup essentially is over.
Vijay Singh, who won the first two events, tied for 44th and earned enough points that all he has to do is complete four rounds at the U.S. Tour Championship in two weeks to collect the $10 million (€7 million) payoff.
But the surly Singh didn't seem terribly grateful.
In a move that took some shine off the tour's new prize, Singh refused to speak to NBC Sports and walked briskly past a group of other media after finishing his round.
Villegas, a 26-year-old in his third year on tour, finished at 15-under 265 and collected $1.26 million (€880,000).
"It's awesome to be here," said Villegas, who wore a solid white outfit accented by a yellow belt and painter's cap. "Hopefully, it's the first of many."
Villegas had been building toward a moment like this in the last few months. He was near the lead going into the weekend at the British Open, rallied to finish fourth in the U.S. PGA Championship, then started the final round last week at the Deutsche Bank Championship one shot behind until faltering.
He had ample opportunity to let this one get away, too.
First came back-to-back bogeys on the front nine, losing the lead to Jim Furyk. But the real test came on the back nine, when Villegas was clinging to a one-shot lead and could not reach the green on the par-4 12th after hitting into a bunker. His third shot came up 12 feet short, but he sank the par putt to keep the lead.
One hole later, he seized control.
Furyk hit his tee shot into a bunker on the par-3 13th and made bogey, while Villegas took yet another aggressive line and holed a 10-foot birdie to build a three-shot lead. Then came a 35-foot birdie putt on the 14th that sent him on his way to victory at Bellerive.
Anthony Kim rallied late to get within two shots, but he sent his approach into the bleachers on the 18th and made bogey for a 67, leaving him a tie for third with Furyk, who shot 70.
Villegas' appeal began two years ago at Miami when he finished in a tie for second behind Tiger Woods before a crowd loaded with Hispanic fans. Then came his "Spider-Man" style of reading putts, contorting his body into a horizontal position to keep his eyes as close to the ground.
Endorsement deals and photo shoots followed, not to mention a strong following of females in his gallery. All he lacked was a U.S. PGA Tour trophy, which he earned over three days in a weather-plagued event.
Despite a few hiccups - such as a four-putt double bogey in the second round on Saturday and three straight misses from inside 8 feet on Sunday - he never buckled.
Villegas went over $3 million (€2.1 million) in earnings for the year and likely will move into the top 20 in the world ranking.
And yes, he still has a mathematical chance for the FedEx Cup.
He moved up to No. 2 in the standings, but even if he wins the U.S. Tour Championship and Singh finishes last, Villegas still would finish 101 points behind. His only hope is to win at East Lake and for Singh to withdraw or get disqualified.
Singh's behavior at the end of his round, however, raised questions how much he cares about a trophy that is part of the tour's so-called "New Era in Golf."
