The Braves snapped a four-game losing streak that put them a half-game behind San Diego in the NL wild-card race. San Diego hosted Cincinnati later Saturday.
The 69-year-old Cox, set to retire at the end of the season, became the fourth major league manager to reach the milestone. He is seeking his 16th postseason appearance.
Lowe (15-12) allowed five hits, walked one and struck out four, improving to 4-0 with a 1.08 ERA in his last four starts. The right-hander has 13 scoreless innings in two games against the Nationals during his winning streak.
Lowe wiggled out of a jam in his final inning after his defense put him in a tough spot. With two out, Ian Desmond grounded to Derrek Lee at first, but the ball squirted under his glove. Adam Dunn flied to center, and Nate McLouth dropped the ball for an other error. But Lowe got Michael Morse to bounce out to end the inning.
The Braves scored four times in the sixth to take a 5-0 lead. They had just seven runs during their losing streak.
Lee doubled in Martin Prado with one out and McLouth followed with an infield single. Gonzalez then hit a drive to left for his 23rd homer.
Yunesky Maya (0-3) allowed five runs, four earned, and eight hits in 5 1-3 innings. The Cuban defector struck out one and walked three in his fourth major league start.
The Nationals had won a season-high four straight.
On Saturday morning, Cox relaxed in the visitors' dugout, talking about the last night he might spend on a major league road trip. He was going to dinner with a friend, and admitted he was a little embarrassed by all the attention his retirement has attracted.
Peter Moylan, Jonny Venters, Craig Kimbrel and Billy Wagner each pitched a scoreless inning for Atlanta, completing a six-hitter.
NOTES: Nationals 3B Ryan Zimmerman missed his third game with a rib injury. Manager Jim Riggleman said he doubted Zimmerman would play on Sunday and could miss the rest of the season. "It could be fine tomorrow or it could be two weeks," Riggleman said. Riggleman said that he wouldn't rest Zimmerman to preserve his .307 batting average. No Washington-based player has hit over .300 since Buddy Lewis hit .317 in 1940 for the Senators. ... Nationals CF Nyjer Morgan played his first game since returning from an eight-game suspension. He went 1 for 5. ... Cox hasn't decided on his starters for next week's series against Florida, and is considering starting some of them on three days' rest. ... The Nationals will honor Cox before Sunday afternoon's game.