Watney, who won a World Golf Championship at Doral in March, closed with a 4-under 66 on Sunday. He goes to No. 10 in the world and leads the FedEx Cup standings and PGA Tour money list for the first time.
K.J. Choi made a charge on the back nine and caught Watney with a 35-foot birdie putt on the 14th. But on the next hole, Choi made double bogey from a terrible spot in a bunker.
Rickie Fowler, who shared the lead with Watney, shot 74 and finished nine shots behind.