Watney finished at 10-under 274 at Bethpage Black, three better than Brandt Snedeker.
The victory in the first of four PGA Tour playoff events vaulted him into the lead on the FedExCup points list and improved his chances for a captain's pick spot on the U.S. Ryder Cup team.
Snedeker also earned Ryder Cup consideration from U.S. captain Davis Love III with his Barclays performance. He carded a 1-under 70 to take second at 7-under par.
Tiger Woods posted a 5-over 76 Sunday, tying for 38th at plus-1.
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