Kyle Wright pitched six innings for his first major league win, helping Atlanta take three of four from Washington.
The Nationals carried a 4-2 lead into the sixth, and Scherzer had already thrown 104 pitches. Manager Dave Martinez sent the three-time Cy Young Award winner out to start the inning, and stuck with him after Dansby Swanson flied out and Nick Markakis singled.
Two pitches later, Duvall blasted his major league-leading ninth homer in September. The drive to deep center was his 14th homer overall this season.
Martinez still didn't change pitchers, and Austin Riley looped a single to right before Albies lashed his third homer to center.
''I had an extra day coming into the start, got two extra days coming up, bullpen's been taxed, threw five innings, I'm thinking there I need to get through the sixth inning,'' Scherzer said. ''We got three of the four right-handed hitters coming up, that's an opportunity for me to go out there and try to get through that inning. There's no reason why I should come out of the game after the fifth inning.''
Scherzer (4-3) struck out 10 while throwing 119 pitches in 5 1/3 innings. He allowed six runs for the first time since yielding seven against Miami on April 20, 2019.
''We get to the sixth inning and it was all about location that inning,'' Martinez said. ''He's our ace. And when you have these conversations and you're watching him and he says he feels good, for me, who else do you want out there in the sixth inning?''
Wright (1-4), who was 0-7 with a 7.86 ERA in 16 career appearances before Sunday, allowed three earned runs and eight hits.
''It took a lot longer than expected,'' Wright said of his first victory. ''I felt like I kind of got away from myself a little bit. Now I'm slowly getting back to where I need to be. I still have a long way to go, but I definitely like the way I am trending.''
The 24-year-old had pitched more than four innings just once in his five previous starts in 2020.
''He's experiencing things and he's figuring himself out,'' Braves manager Brian Snitker said. ''It's really good. I've had multiple talks with him about how good his stuff is. How good he can be. He doesn't have to take a backseat to anybody and you saw it today.''
Atlanta added two insurance runs in the ninth on Marcell Ozuna's RBI single and Travis d'Arnaud's fielder's choice grounder.
Four Braves relievers combined for three shutout innings of relief. Atlanta improved to 21-0 this season when leading after six innings, while Washington fell to 0-21 when trailing after six innings.
''We've gotten some really positive things that happened these last four days here, with the rotation, getting Ozzie back,'' Snitker said. ''I like where we're at. Bullpen, it was good to see those guys step up today. We had a bunch of main-line guys down we've been counting on a lot in the bullpen and those guys did a great job piecing that thing together.''
Asdrubal Cabrera hit his sixth homer of the year for Washington.
Braves: LHP Cole Hamels (triceps tendinitis) is listed as the starter for Wednesday's game at Baltimore. Hamels has not pitched since agreeing to a one-year contract in the offseason.
Nationals: OF Adam Eaton, who was scratched from Saturday's lineup with back spasms, led off in the series finale. He was 2 for 4 with a walk and a stolen base.
SUNDAY FUN DAY
Atlanta improved to 8-1 on Sundays this season. It has outscored opponents 69-25 on Sundays.
Braves: RHP Touki Toussaint (0-1, 7.89 ERA) faces Baltimore for the first time as Atlanta continues its road trip by opening a three-game series Monday against the Orioles.
Nationals: Washington begins its final road trip of the season Tuesday when it opens a two-game series at Tampa Bay. RHP Anibal Sanchez (2-4, 6.34 ERA) makes the start for the Nationals.
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