The 23-year-old Kim's win was his second this year on the PGA Tour. He won the Wachovia Championship two months ago.
Kim finished with a12-under 268 on the Congressional course. Fredrik Jacobson also closed with a 65 and placed second at 10-under 270.
"Winning (on the tour) is so tough that any time you get an opportunity to be in the hunt it feels great," Kim said. "And to capitalize on the two chances I've had of late feels wonderful."
Six players shared third place at 9-under 271: Rod Pampling (65), Jim Furyk (66), Dean Wilson (67), Robert Allenby (67), Tommy Armour III (69) and Nick O'Hern (69).
Tom Pernice, who led after three rounds, slipped to a 2-over 72 and ended up in a tie for ninth place.