Francisco Lindor had three hits and three RBIs as New York took the opener 8-5, and the Mets stretched their NL East lead to 5 1/2 games.
Mets fans taunted the second-place Braves in the ninth inning of Game 2 by performing the tomahawk chop, a tradition at games in Atlanta despite complaints from some Native American groups that the chant is degrading.
''I'm not going to tell you I didn't notice it,'' New York manager Buck Showalter said. ''Of course I did. We all have our personal opinions on stuff like that.''
Pete Alonso had three singles, including one with the bases loaded to match Yankees star Aaron Judge for the major league lead with 93 RBIs. The Mets swept their second doubleheader against Atlanta this season and opened their biggest division lead since June 21. They are 11-3 in seven twinbills this year, including four sweeps.
''Total team wins in both games,'' Scherzer said after earning his 198th career win. ''We're just playing great baseball right now.''
Lindor reached twice in the late game and scored on shortstop Dansby Swanson's throwing error as Max Fried (10-4) was nearly injured on the play.
New York (69-39) is 30 games over .500 for the first time since finishing 97-65 in 2006.
Scherzer (8-2) allowed four hits, including two doubles to Travis d'Arnaud. The three-time Cy Young Award winner produced his fourth scoreless outing this season and third since returning from an oblique injury July 5.
''He's a great concentrator and he treats every hitter in the same lineup with the same respect,'' Showalter said. ''And he's got a plan. It might not always be perfect, but when he's got command of his pitches and he can execute - and he's a student of the game.''
Scherzer retired his final nine hitters and ended the seventh with a flourish. He struck out the side on 15 pitches, getting Eddie Rosario to whiff at a cutter before pinch-hitter William Contreras and Marcell Ozuna swung through sliders.
''They're a great team, great lineup,'' Scherzer said. ''For us to show up and bring the energy and go out there and beat them, that's great. It's great to get these wins, but it's not over yet. We know how good they can play, and they can get hot.''
The strikeout of Ozuna pulled Scherzer into a tie for 14th on the career list with former Detroit Tigers teammate Justin Verlander at 3,140.
''He's one of the best pitchers in baseball,'' Fried said. ''Has been for a long time.''
Scherzer recorded his 109th career double-digit strikeout game and fifth this year. He did not issue a walk for the fourth time this season.
''His consistency is unbelievable,'' Alonso said.
New York has won three of four in the five-game showdown and is 13-0-2 in series against NL East rivals this season.
Ronald Acuna Jr hit an RBI single off Mychal Givens in the eighth and Contreras homered in the ninth, but Atlanta dropped to 4-7 in the season series against the Mets and committed three errors.
Swanson made two errors and third baseman Austin Riley had a throwing error in the sixth on a soft grounder by Darin Ruf.
Fried allowed four runs (two earned) and six hits over six innings in his 100th major league start. He also was shaken up after a hard fall during New York's three-run third.
After Alonso hit a bloop single, Ruf hit a grounder to first baseman Matt Olson, who got the force at second. Swanson's return throw bounced and caromed off Fried's chest at first and went into foul territory.
Fried slipped and fell face-first, and his pitching shoulder and head hit the ground hard as he attempted to get Lindor at home. The left-hander remained in the game.
''Just kind of fell and kind of just whipped my neck and hit my head,'' Fried said.
New York scored three in the third and then capitalized on Riley's error in the sixth. Riley's throw went past Olson on Ruf's soft infield single, moving Alonso to third.
The slugger broke for home when Mark Canha hit a chopper to Riley down the line. He made a high throw and Alonso was initially called out by plate umpire Manny Gonzalez on an acrobatic tag by d'Arnaud. But replays showed Alonso's foot grazed the plate before d'Arnaud could apply the tag, and the call was overturned.
After Givens allowed Acuna's RBI single in the eighth, pinch-hitter Tyler Naquin hit an RBI single and scored on a suicide squeeze by Tomas Nido.
Showalter got his 1,620th win in the nightcap to move past Ralph Houk into 20th place on the career list. Houk managed the Yankees, Tigers and Red Sox and went 1,619-1,531 in a career that began in 1961 and lasted through 1984.
Braves: D'Arnaud was lifted in the seventh after a trainer checked him during the replay challenge following his collision with Alonso in the sixth. After the game, X-rays on d'Arnaud's lower right leg were negative
Atlanta rookie RHP Spencer Strider (5-3, 2.91 ERA) opposes New York RHP Jacob deGrom (0-0, 1.80) on Sunday in the finale of the five-game series. DeGrom makes his 200th career start and first at home since July 7, 2021.
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