Freeman's shot in the first inning gave the Braves a quick 3-0 lead and Heyward's bases-clearing double in the next frame iced the victory.
Mike Minor (10-10) tossed six solid innings, allowing two runs on only two hits and a walk, while striking out six. The left-hander won his fourth straight decision for the National League wild card-leading Braves, who evened their three-game series.
Phillies starter Roy Halladay (10-8) was roughed up for seven runs on five hits, lasting just 1 2/3 innings.
Ryan Howard socked a solo homer for Philadelphia.