The Red Sox went 1-5 on the six-game homestand. They begin a three-game series against the Marlins in Miami on Monday with Josh Beckett scheduled to start against his former team. After that, they travel to Wrigley Field for a three-game set with the Cubs.
The Sox also dropped two out of three to the Orioles to open the homestand.
"It's just not very good, we didn't play well," said second baseman Dustin Pedroia. "We faced some tough pitching, we didn't swing the bats as well as we would have liked. We'll go on the road and continue to play and play hard."
Closer Alfredo Aceves picked up his fourth loss after allowing one run in the ninth inning. He walked pinch-hitter Bryce Harper, who scored on a two-out double to right by Roger Bernadina.
Frustrations boiled over in the bottom of the ninth when home-plate umpire Al Porter ejected Valentine for arguing balls and strikes.
"We've got guys busting their butt, battling their butt off. It's not right. Good umpires had a real bad series this series," Valentine said. "Real bad series. And it went one way. There should be a review."
The loss spoiled a good outing from starter Jon Lester. He struck out nine in seven innings, scattering six hits and allowing three runs with two walks. Lester did not return for the eighth after throwing 107 pitches (67 strikes).
The left-hander was saddled with a no-decision and remained unbeaten in his career against Washington.
The Red Sox are two games under .500 for the first time since they were 19-21 on May 19. They are in last place in the American League East. The last time the Sox were in the division cellar this late in the season was in September 1997.
"Nobody has been in this situation here. Nobody has lost before like this. It's all new," Lester said. "I can speak for myself: I hate going out there and losing, regardless of if I'm pitching or not. I know guys down there are frustrated and rightly so."
Danny Espinosa's two-run double in the seventh gave the Nationals a brief 3-2 lead. He hit an arching fly ball that glanced off the Green Monster, just out of reach of Darnell McDonald's outstretched glove.
"It seems like it's just Groundhog Day every day, every start for me. I can't seem to get a break," Lester said. "I feel like I threw the ball good today. A fly ball to left, a 300-foot fly ball -- different ballgame.
"It's just, today, a 300-foot fly ball is the difference in the game. It's bad luck in some games. It's playing bad in other games. It's pitching bad. It's not playing good defense. Whatever it is, it seems to come back and bite us."
Boston tied the game at 3 in its half of the frame on an RBI groundout from Scott Podsednik. The Red Sox had a chance to take the lead in the eighth. David Ortiz singled and Will Middlebrooks walked to put a man in scoring position, but Ryan Sweeney grounded out to first.
Lester avoided a big inning in the third after loading the bases on a single and two walks. He went to a full count against Michael Morse, but struck him out on an inside fastball.
That proved to be an important out as Pedroia tied the game at 1 with an RBI in the bottom of the frame. He also broke out of a 2-for-20 slump with a single in the first.
Ortiz launched a solo home run to lead off the fourth, turning on a 1-0 pitch and sending it into the Nats' bullpen. The slugger's team-leading 14th homer gave the Sox a 2-1 advantage. Ortiz finished 3-for-4 with a double to break out of a 2-for-17 slump.
"David swung the heck out of the bat," Valentine said. "He's been a very consistent offensive force for us playing like an All-Star."
Nationals starter Jordan Zimmermann also had a strong outing. He allowed three runs on seven hits, striking out seven against two walks.
"[He] pitched one hell of a ballgame and I feel bad that we didn't get the win for him," said Washington manager Davey Johnson. "It was another great ball game. It was a strong game. In the seventh inning he gave up two leadoff hits, but he got us out of there with just one run. But I sure would have liked to have gotten the win for him."
Boston's Nick Punto contributed in his third start of the year at shortstop, scoring in the third after a leadoff walk. He singled in the seventh and finished 1-for-3.