Washington has now lost eight straight games dating back to last season.
With one out in the 10th and left-hander Joe Beimel on the mound, Kelly Johnson singled to right field on a 1-2 pitch to drive in Jordan Schafer.
Beimel was signed by the Nationals to get left-handed hitters out. But Atlanta's left-handed hitters went 2-for-3 in the game against him.
"I pitched both innings with the leadoff guy on, so it's kind of tough in both innings to do that, especially when you are playing for one run. You don't have much room for error," Beimel said.
After the game, manager Manny Acta appeared stunned that the Nationals left 16 runners on base. The team had the bases loaded four times and couldn't put the Braves away.
"It's a funny game. I don't think I ever seen a team have the bases loaded four times and not be able to score a run," he said. "We can't blame anybody but ourselves. We battled, but we played hard. We just have to continue to fight, and we'll come out of it. It was tough, because we had plenty of opportunities."
Left-fielder Adam Dunn didn't pull any punches how he felt about the lack of offense on the club. The players and the coaching staff must find a way to make it better.
"You can't win games like that," Dunn said. "That's something that has to be addressed. We have good enough people -- not just players, but the coaching staff -- to address that problem. That's why we are not winning these games."
Asked how to address the problem, Dunn said, "You have to put an emphasis on it and bear down. That's the time when you bear down and have a plan. Those are the important times in baseball. It's tough to win without scoring runs, and you are not going to get a lot of bases-loaded walks."
It was a game that went back and forth. Washington took a 1-0 lead in the third inning when Ryan Zimmerman hit a Derek Lowe pitch over Jeff Francoeur's head in right field for an RBI double and put runners on second and third with one out. But both Nick Johnson and Elijah Dukes struck out to end the threat.
"We had our best hitters up. We didn't get a ball up in the air," Acta said. "We have to continue to plug away. There isn't a switch to turn on and off."
But the Braves took a two-run lead in the bottom of the inning. With runners on first and second and one out, Yunel Escobar hit Shairon Martis' 2-0 pitch over the left-center-field wall.
There was a two-hour, two-minute rain delay before the Nationals' bats came to life against Atlanta's relievers. With the Braves leading, 4-1, and Buddy Carlyle on the mound, Cristian Guzman singled to right-center field to drive in Willie Harris.
Right-hander Peter Moylan entered the game and gave up an RBI double to Zimmerman. Left-hander Eric O'Flaherty came in to face Dunn, who hit a hard grounder toward the first-base bag. The ball hit first baseman Casey Kotchman in the face and bounced near the dugout, allowing Zimmerman to tie the score at 4.
The Nationals had a golden opportunity to take the lead in the top of the seventh inning off right-hander Jeff Bennett. They had the bases loaded with one out, but Lastings Milledge hit into a double play to end the inning.
"We had our opportunities. We are not capitalizing on them," Dunn said.
Atlanta scored the go-ahead run in bottom of the seventh inning off right-hander Saul Rivera. He was able to get two quick outs, but after Brian McCann doubled and Kotchman walked, Francoeur singled up the middle to drive in McCann.
Washington would tie the score at 5 off Mike Gonzalez in the ninth inning, when Milledge hit a liner off the closer's glove, allowing Nick Johnson to score.
Bill Ladson is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.