The Braves (96-51), who clinched their sixth straight NL East title on Wednesday, removed star right fielder Ronald Acuna Jr. from the game in the eighth inning due to right calf tightness.
Miami (76-72), battling for an NL wild-card playoff berth, got 13 hits and improved to 2-9 against the Braves this season.
Miami beat former Marlins reliever Brad Hand (4-2), who allowed four runs in one-third of an inning.
The win went to reliever A.J. Puk (6-5), and the save went to Tanner Scott, who hasn't allowed a run since July 31. It was his ninth save of the year.
Arraez, who leads the majors with a .349 batting average, had the first multi-homer game of his career. He went 2-for-5 with two RBIs.
Michael Harris II homered for the Braves, his 17th of the year.
Miami opened the scoring on just the fifth pitch seen by Marlins' hitters as Arraez pulled a 1-2 sinker over the fence in right.
The Marlins added two more runs in that first inning. Bryan De La Cruz lined an RBI single off the glove of second baseman Ozzie Albies, and Jesus Sanchez followed with a run-scoring triple to the gap in right-center.
Miami made it 4-0 in the second as Stallings doubled and scored on Jake Burger's two-out single.
Atlanta cut its deficit to 4-2 in the third. Harris started the rally by homering on the inning's first pitch. The Braves kept the rally going as Acuna singled and scored from second on Austin Riley's single.
The Braves went on to load the bases with one out in that same inning. But Eddie Rosario (groundout) and Travis d'Arnaud (popup) failed to push another run across.
Atlanta closed its deficit to 4-3 in the fourth as Orlando Arcia doubled, advanced on Harris' groundout and scored on Acuna's sacrifice fly.
The Braves tied the score in the fifth as Riley doubled and scored on Rosario's sacrifice fly.
Atlanta took a 6-4 lead in the sixth on Albies' two-run single.
In the seventh, Arraez homered to make it 6-5. Then, with two outs and none on, the Marlins scored four more runs, getting Garrett Hampson's RBI and Stallings' bases-loaded two-bagger.
—Field Level Media