Anthony Rendon also had two hits and drove in two runs for Washington, extending his hitting streak to 10 games and helping the Nationals earn a split of the series after Saturday's game was rained out. Adam Eaton and Juan Soto each had three hits.
"It's part of it. We play outdoors," Nationals manager Dave Martinez said of the rain. "But the boys hung in there. They were all pretty loose in the clubhouse, honestly. Watching Shark Week. So, it was good."
The start of the game was delayed 1 hour, 55 minutes by rain, and another downpour stopped play for almost 100 minutes between the sixth and seventh innings.
Two days after a heated exchange with teammate Stephen Strasburg during Friday's 8-5 loss, Scherzer (13-5) allowed two runs and eight hits in his third straight win. The three-time Cy Young Award winner has pitched six or more innings in his last 19 starts, though the Braves made him work for it.
"A division team, they know everything I got," Scherzer said. "They absolutely grind apart every at-bat. It's really hard to put them away. Our defense played outstanding today."
Speaking with reporters for the first time since Friday's dugout disagreement with Strasburg, Scherzer shed no new light on the exchange, saying only: "Look, it was miscommunication, settled it. It's over. End of story."
Kelvin Herrera got five outs for his first save with Washington.
Atlanta's Mike Foltynewicz (7-6), an All-Star who spent much of this week in Washington, gave up four runs and nine hits over 5 2/3 innings.
"Just waiting around this long, it's kind of irritating," he said of Sunday's delays. "I'm ready to get out of D.C. It's been a while here."
Harper singled in Eaton to give Washington a 4-2 lead in the sixth. Matt Adams added another RBI single in the seventh, and Harper hit a solo drive in the eighth for his 24th homer.
Scherzer was staked to an early 3-0 lead and then got some help from his defense.
Atlanta rookie Ronald Acuna Jr. led off the third with a drive off the wall in center, but he was thrown out by Harper while trying for a double. With a runner on first in the fifth, Freddie Freeman's blast to right was chased down by Eaton on the warning track.
Then in the seventh, Michael A. Taylor made a leaping catch at the wall in center to rob Dansby Swanson of extra bases with one runner on.
Washington got off to a fast start with three runs in the first. Rendon drove in Eaton and Harper with a triple down the right-field line, and then scored on Soto's groundout.
Swanson drove in Atlanta's runs with a groundout in the second and a single in the fourth, but the Braves couldn't land any big blows on Scherzer.
"Got his pitch count up, but that guy never gives in," Braves manager Brian Snitker said. "He's an unbelievable competitor, as good as there is in the game."
Saturday's game will be made up Aug. 7 as part of a split doubleheader, with games beginning at 1:05 and 7:05 p.m.
The Nationals acquired minor league right-hander Jacob Condra-Bogan from the Kansas City Royals in exchange for outfielder Brian Goodwin. The Nationals also recalled lefty Sammy Solis from Triple-A Syracuse.
Braves: All-Star 2B Ozzie Albies, who left Friday's game with right hamstring tightness, got the day off.
Nationals: RHP Sean Doolittle (left toe inflammation) experienced extended soreness after throwing off the mound Friday. An MRI Saturday revealed a stress reaction, comparable to a bone bruise, in the bridge of his foot and he is wearing a walking boot. ... RHP Koda Glover (right shoulder tendinitis) was reinstated from the 60-day DL and optioned to Triple-A Syracuse.
Braves: LHP Sean Newcomb (8-5, 3.51 ERA) pitches the opener of a two-game series in Miami on Monday. He already has beaten the Marlins twice this season, allowing one run in 12 innings.
Nationals: LHP Gio Gonzalez (6-6, 3.72 ERA) opens a three-game series in Milwaukee on Monday night. He is 2-4 with a 4.93 ERA in nine career starts versus the Brewers.
More AP baseball: https://apnews.com/tag/MLBbaseball
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