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With Cla Meredith (0-2) on the mound, Willingham drilled a 2-1 pitch just over the wall in left-center for the win.
Roger Bernadina hit a three-run triple while Nyjer Morgan added two hits and a run scored for the Nationals, who took the last two games of the set after dropping the opener on Friday.
John Lannan went 5 1/3 innings and scattered one run on two hits with three walks and two strikeouts. Doug Slaten (2-0) got the win for throwing a perfect top of the 10th.
Matt Wieters and Julio Lugo each drove in a run for the Orioles, who have dropped seven of nine. Kevin Millwood gave up three runs on eight hits with a walk and eight strikeouts over his 6 1/3-inning start.
With Washington holding a two-run lead in the ninth, Matt Capps came out to close the game, but he was unable to. After getting Ty Wigginton to strike out, Luke Scott singled and Adam Jones doubled. Wieters then grounded out to score Scott for a one-run game, and Lugo blooped a single into right to tie the contest. It was Capps' first blown save in 17 chances this season.
Baltimore got on the board in the first as back-to-back singles from Corey Patterson and Nick Markakis to start the inning was followed by a double play groundout from Miguel Tejada that scored Patterson.
Washington answered in the bottom of the frame. Morgan led off with a single and Cristian Guzman reached base on a bunt. After the next two batters recorded outs, Willingham was hit by a pitch to load the bases, and Bernadina followed with a triple to center that went off Jones' glove for a 3-1 lead.
The Nationals threatened in the fourth as they put two men on base with one out, but Guzman flied out andRyan Zimmerman looked at strike three to end the frame.
The Orioles, meanwhile, didn't get another runner to second base until the sixth. Patterson led off with a walk and then stole second. After Markakis flied out, Drew Storen took the mound and got Tejada to fly out, but Wigginton walked. Storen, though, struck out Scott to end the threat.
Storen stayed on for the seventh and set Baltimore down in order while Sean Burnett and Tyler Clippardworked the eighth inning.
Washington hits the road for its next 10 games and starts a three-game set in San Francisco on Tuesday...Baltimore hosts Oakland for a three-game series starting on Tuesday...The Nationals improved to 114-118 in interleague play while the Orioles fell to 102-130 in interleague play.