The Nationals lost a game they believe they should have won, but hope they won't lose starter Tom Gorzelanny.
The Nationals scored six runs off Braves ace Jair Jurrjens but couldn't hold a 6-2 lead.
"Jurrjens has probably been one of the best pitchers in the league all year long," Washington reliever Tyler Clippard said. "We got to him really good. Our offense did a great job today. This is definitely a game we've got to win."
Clippard recorded five straight outs, four on strikeouts, before giving up Nate McLouth's tying homer in the eighth. The Braves then won it in the ninth.
Ryan Mattheus (2-1) walked pinch-hitter Brooks Conrad to start the bottom of the ninth. Jordan Schafer sacrificed Conrad to second before Conrad was thrown out at third on Prado's grounder to shortstop Ian Desmond. Prado stole second base before Mattheus issued an intentional walk to Brian McCann, who hit a three-run homer in the fifth.
"I hadn't been in that situation very often, so when they walked Mac, I got a little extra excited," Freeman said. "I wouldn't pitch to him, either."
Freeman lined a 1-0 pitch into right field and was soon in the middle of a celebration between first and second base after Prado easily scored the winning run.
Mattheus said his biggest mistake "was most definitely the leadoff walk."
"Once that happened right from the get-go, that put them in the driver's seat," Mattheus said.
Gorzelanny left the game with a twisted right ankle in the third inning. He limped off the field after scoring from first base in a home-plate collision with McCann on Roger Bernadina's triple.
Nationals manager Davey Johnson said he believes Gorzelanny, with the help of an off day on Thursday, can make his next scheduled start against the Dodgers on Friday.
"He's got an extra day, so hopefully he'll be able to make his next start in L.A.," Johnson said.
Johnson said his bullpen was stretched after Gorzelanny's early departure.
"The bullpen, I pushed it to the limit," Johnson said. "They all did a good job. Unfortunately, I had to expand their roles, something they're not used to."
Craig Kimbrel (3-2) gave up a walk and a single in a scoreless ninth.
Danny Espinosa had three hits, including a two-run homer in the sixth that gave Washington an 8-7 lead. Espinosa, who also had a single and a run-scoring triple, drove in Bernadina with his 17th homer off George Sherrill.
McCann's 16th homer was the highlight of Atlanta's five-run fifth.
Jurrjens gave up a season-high six runs on eight hits and two walks in five innings. He allowed a combined 11 baserunners in the third and fourth but was allowed to pitch through the Nationals' four-run fourth.
Jurrjens worked a perfect fifth before leaving the game for a pinch-hitter in the bottom of the inning. His ERA climbed from 1.87, best in the major leagues, to 2.26, still good enough to lead the NL.
It was the second straight game in which a Braves starting pitcher set a season high for runs allowed. Tommy Hanson gave up five runs in Atlanta's 5-2 loss to the Nationals on Saturday night.
Gorzelanny issued three walks in the Braves' two-run first inning. Gorzelanny and Johnson argued when second base umpire Dana DeMuth called a ball for Gorzelanny putting his pitching hand to his mouth while on the mound.
The call gave Dan Uggla a walk, loading the bases, before Gorzelanny's wild pitch allowed Prado to score from third.
After Gorzelanny scored on Bernadina's third-inning triple, Bernadina kept running and scored on Uggla's wild relay throw for an error. The throw forced McCann to move up the third-base line and set up the collision with Gorzelanny.
The Nationals had six hits in the four-run fourth, including a two-run triple by Desmond. Espinosa added another triple off the top of the wall in center before scoring on Ryan Zimmerman's double.
NOTES: Clippard has allowed eight homers. ... 3B Chipper Jones, on the 15-day DL following arthroscopic surgery on his right knee July 9, will not accompany the Braves on their four-game series at Colorado. He still hopes to come off the DL the first day he is eligible, on July 24. ... Braves rookie Wilkin Ramirez made his second straight start and had a double.