The game had been scheduled for Monday night but was postponed following the shootings in which 13 people, including the gunman, were killed at the nearby Navy Yard in Washington.
The Nationals scored three times in the first inning but were stymied after that, having 18 consecutive batters retired from the second through eighth innings.
Braves closer Craig Kimbrel (3-3), who leads the majors in saves, entered the ninth with a 5-3 lead but walked Adam LaRoche to open the inning and Wilson Ramos followed with a single -- the first Washington hit since the second inning. Kobernus was inserted as a pinch-runner for Ramos.
Rendon worked Kimbrel for another walk, loading the bases and LaRoche scored on a groundout. Denard Span, who in the second extended his hitting streak to 27 games, sent a bouncer up the middle that went between the legs of shortstop Andrelton Simmons, and Kobernus and Rendon both scored.
The Nationals opened the game with two walks and a double in building a 3-0 lead but Atlanta chipped away with single runs in the sixth and seventh and a two-run home run by Evan Gattis in the eighth. The Braves went up 5-3 by scoring a run on an error in the ninth.
Ian Krol (2-1) was awarded the win with one-third of an inning of relief in the ninth.
It was just the fifth time in 17 games this season that the Nationals beat the Braves, who entered Tuesday 6-0 in Nationals Park this season.