The blast capped a four-run rally and broke a 4-4 tie with one out in the top of the ninth against losing pitcher Manny Acosta (3-3).
The big-hitting shortstop also launched a solo homer in the third and scored three times.
Mike Rabelo's second hit, a two-run homer, created the tie and Mike Jacobs had one RBI for the Marlins, who snapped a three-game losing streak.
The winner was Justin Miller (2-2) after two innings of scoreless relief.
Kevin Gregg earned his 11th save this season.
Yunel Escobar and Greg Norton had one RBI apiece for the Braves, who entered the four-game series Monday on a three-game losing streak.
Atlanta learned before the contest that former ace John Smoltz is due for season-ending shoulder surgery next week.