New York's bullpen held on despite shaky performances by Bobby Parnell, J.J. Putz and Francisco Rodriguez, who returned from back spasms to get his 13th save in 13 chances.
Carlos Beltran was back in center field after moving to designated hitter for the weekend series at Boston's Fenway Park because of a sore right knee, and Ramon Martinez played shortstop despite a sore lower back.
Already without first baseman Carlos Delgado (hip surgery) and catcher Brian Schneider (back) because of longterm injuries, the Mets were missing shortstop Jose Reyes (calf) and right fielder Ryan Church (hamstring).
Reyes, sidelined for the eighth time in 11 games, could be put on the disabled list if he doesn't improve by Friday. An MRI on Church showed no damage but he wasn't up to playing.
On a night when the Mets wore red caps as part of Major League Baseball's Memorial Day initiative, there were 16 walks, including nine by New York pitchers.
Beltran went 2 for 3 and was thrown out at the plate trying to score in the first inning, Martinez was 0 for 3 with a sacrifice fly.
With the score 1-1 in the sixth, Luis Castillo doubled leading off against John Lannan (2-4) and Beltran walked. Pitching coach Randy St. Claire made a trip to the mound, and Sheffield sent the next pitch deep to left field.
A fan reached out just before the fence reaches the 15-foot, 8½-inch mark, and the ball bounced back to the field. Third base umpire Adrian Johnson signaled a home run, and Washington manager Manny Acta came out and argued.
All umpires except Dan Iassogna, who was working at first, went under the stands to consult video replay. After a 6-minute wait, crew chief Larry Vanover came back to the field and signaled home run, Sheffield fourth this season and No. 503 in his big league career.
Martinez added a sacrifice fly off Jesus Colome for a 5-1 lead.
Parnell retired just one of five batters he faced in the bottom half and walked three, including Johnson with the bases loaded.
Adam Dunn, who hit a grand slam on Sunday against Baltimore's Jamie Walker, popped a short flyout against Pedro Feliciano. Putz fell behind 3-1 in the count against Austin Kearns, who fouled off a pitch and hit an inning-ending groundout. Putz walked his first two batters in the eighth, and Rodriguez pitched around a hit and a walk in the ninth.
Washington, coming of a 2-9 homestand, became the first team to make second trip to Citi Field even though the Nationals haven't hosted the Mets this year.
Lannan, a Long Beach, N.Y., native who is the only non-rookie in Washington's rotation, gave up five runs, eight hits and four walks in five-plus innings for the Nationals, a major league worst 13-31.
Daniel Cabrera, dumped from the rotation after going 0-5 in eight starts, entered in the seventh for his second relief outing in 156 major league appearances, his first since his rookie season in 2004. He got just two outs and walked the bases loaded before Jason Bergmann got Fernando Tatis to hit into a forceout.
Johnson was back after missing Sunday's game with a stomach ailment that required a hospital trip and went 1 for 3 with two walks and an RBI.
Beltran doubled with two outs in the first and was thrown out at the plate by Austin Kearns trying to score on Sheffield's single to right. Wil Nieves' RBI single then put the Nationals ahead in the second, but Beltran's RBI single tied the score in the third.
Note: Sheffield's homer was the 32nd in 21 games at Citi Field, a fraction of the 87 in 23 games at the new Yankee Stadium. ... The last rubble of Shea Stadium was removed during the 10-game trip, giving the Mets a full parking lot surrounding Citi Field. ... Ryan Zimmerman singled in the third and has reached base safely by a hit or a walk in 43 consecutive games, topping the Montreal/Washington season franchise record set by Tim Raines in 1986. He is three shy of Rusty Staub's overall franchise record.
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