Derek Lowe (2-0) backed the Braves' attack with six innings of one-run ball, overcoming seven walks to hand the Giants their first loss of the season after a 4-0 start.
Heyward's home run off San Francisco starter Todd Wellemeyer (0-1) came in the sixth inning and was hit just far enough to get over the left field wall and tie the game at 1-1.
His RBI single off Dan Runzler in the seventh got past a diving third baseman Pablo Sandoval, giving Atlanta a 4-1 lead.
Juan Uribe and Aaron Rowand each collected an RBI as the Giants offense was limited to just six hits.
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