With the Braves trailing 3-2 heading into the ninth, Chipper Jones greeted Mike Dunn (0-3) with a double and went to third on a wild pitch.
Freeman then belted 1-1 pitch over the center field wall for the walk-off game-winner, lifting Atlanta into a National League wild card berth with its 15th win in 21 games.
Jones and Dan Uggla also drove in runs as the Braves returned to the playoffs for the first time since 2010 following an epic collapse at the end of last season.
Craig Kimbrel (3-1) earned the victory with a scoreless top of the ninth.
Kris Medlen started and allowed three runs over seven frames. The Braves won their 22nd straight game in which the right-hander has started, tying a major league record.
Donovan Solano bashed a pair of homers, driving in three runs for the Marlins.