Upton's 23rd homer to left-center came on a 2-2 pitch from Ian Krol (1-1).
Scott Downs (2-0) pitched a scoreless 10th for Atlanta.
Washington's Bryce Harper was hit by pitches in the fourth and eighth innings. Home plate umpire Marty Foster warned both benches after Luis Avilan hit Harper on his shoulder in the eighth.
Washington's players rose to the top of the dugout but didn't come onto the field.
The Braves, who swept a three-game series at Washington on Aug. 5-7, lead the season series 11-3, including six straight wins.
Less than two weeks ago, both benches emptied when Harper was hit by Julio Teheran in the Braves' 2-1 win at Washington on Aug. 6.
Downs threw an inside pitch past Harper to the backstop before walking Harper with one out in the 10th. Jayson Werth hit into a double play to end the inning.
Jason Heyward had two hits and scored one run for NL East-leading Atlanta, which stretched its lead over the second-place Nationals to 15 1/2 games.
Both rookie starting pitchers delivered strong performances.
Atlanta's Alex Wood gave up one run and five hits and no walks and a career-high nine strikeouts in 6 1/3 innings.
Washington's did not allow an earned run, but was hurt by three errors. Jordan allowed two runs, both unearned, and seven hits and three walks in six innings.
Washington manager Davey Johnson said before the game the Nationals had something to prove.
"We need to show them that they're not better than us," Johnson said.
The Nationals' defense didn't cooperate with Johnson. Washington's errors led to unearned runs in the first and third innings.
Heyward led off the first inning with a single and took off for second base on ball four to Upton.
Washington catcher Wilson Ramos made an unnecessary and wild throw to second base for an error, allowing Heyward to advance to third before scoring on Freddie Freeman's double play grounder.
Paul Janish, starting at second base after the Braves announced Tyler Pastornicky would need season-ending knee surgery, singled to lead off the third.
After Janish advanced to third on Heyward's single, shortstop Ian Desmond fielded Upton's grounder and threw to second to force Heyward. Second baseman Anthony Redmon attempted to complete the double play, but threw wild to first for an error, allowing Janish to score for a 2-0 lead.
There was no reaction from Harper when he was hit by a pitch from Wood to lead off the fourth.
Harper calmly jogged to first base and then made a comment to Freeman at the bag, prompting both to laugh. Harper advanced to third on Werth's single and scored when Desmond hit into a double play.
Harper wasn't laughing after he was hit by Avilan's pitch in the eighth following a double by Ryan Zimmerman. Luis Ayala replaced Avilan and gave up a single to Werth as the Nationals pulled even at 2-2.