The 31-year-old has endured a poor year on tour but put that behind him to register a three-shot victory after a closing 69, with fellow American Brandt Snedeker in second place at Bethpage State Park, Farmingdale.
Garcia was seeking back-to-back triumphs after winning at the Wyndham Championship last Monday, but he went from the top of the leaderboard at the start of the day to a tie for third alongside Dustin Johnson after a four-over 75.
US captain Davis Love III is due to name his 12 on September 4 for the match against Europe at Medinah, starting on September 28.
"I've been working hard," said Watney. "I'm very pleased how I drove the ball down the stretch. Any time you win it's great for your confidence. I'm so thrilled and very proud of this week."
The win moves Watney into first place in the PGA Tour's playoff points race with three more FedEx Cup events to play.
Like Watney, Snedeker is trying to land a spot on the US Ryder Cup team. He shot a one-under 70 and took second at seven-under par.
Third-round leader Garcia, aiming for back-to-back tournament wins, shared third with defending champ Dustin Johnson, who fired a three-under 68 to reach a six-under 278 total. Garcia was three over par on the back nine Sunday.
Tiger Woods had a day he would like to forget. Woods, who lost his PGA Tour playoffs points race lead, posted a five-over 76 and finished in a tie for 38th, stumbling down the stretch to shoot 40 on the back nine.
A 10-foot birdie putt on the 14th had allowed Watney to take the wind out of the sails of his challengers.
He dropped a stroke with a bogey on 16 and then made par on 17, but Garcia shot a bogey on 18, allowing Watney to close out a comfortable victory at the 18th.
"I made more putts than I made all year," Watney said.
Beating one of the most difficult fields of the year on a demanding course puts Watney in contention to be one of four captain's picks for the American team that will compete in the Ryder Cup September 28-30 in Chicago. Davis Love III will announce his choices after next week's playoff tournament.
"The Ryder Cup is out of my control," said Watney.
"All I can do is try and get ready to play next week and see where the chips fall. I'm thinking about it much more now. Someone told me Davis wanted a hot player."
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