The Nationals, who lead the majors with 103 losses, have a five-game winning streak, their second-longest string of the year.
The Braves have lost four in a row. They were eliminated from the NL wild-card race Thursday.
Livan Hernandez (9-12) earned only his second win in his last nine decisions, giving up nine hits and three runs in 6q innings. He was 7-8 with the New York Mets before signing with Washington on Aug. 25.
Mike MacDougal pitched the ninth for his 20th save.
Derek Lowe (15-10) gave up five earned runs on eight hits and five walks in 4w innings. He finished the season with a 4.67 ERA, his highest since posting a 5.42 ERA in 2004, his last season in Boston.
Lowe's ERA was under 4.00 for four consecutive seasons with the Los Angeles Dodgers, including a 3.24 mark in 2008.
The Nationals' first five hits off Lowe were for extra bases, including a second-inning homer by Desmond. David Ross had a two-run double for Atlanta in the bottom half.
Washington took a 4-2 lead in the third. Justin Maxwell led off the inning with a triple. Desmond added a two-run triple in the right-field corner.
The Nationals added two runs off Lowe in the fifth. With one out, Ryan Zimmerman singled and had to scramble back to first when Nate McLouth made a running catch at the top of the center-field wall on a drive by Josh Willingham.
Lowe walked Desmond and gave up a single by Alberto Gonzalez that drove in Zimmerman. Desmond scored when left fielder Garret Anderson's throw skipped past Ross at the plate. Anderson was charged with an error.
Chipper Jones, who won the NL batting title last season by hitting .364, is 100 points below that mark with two games left. He was 0 for 5 to fall to .264. Jones drove in McLouth with a seventh-inning groundout.
Second baseman Martin Prado had four hits for Atlanta, his third four-hit game of the season.