Ray allowed just four hits and an unearned run in eight innings. Caleb Kilian entered with a 3-1 lead in the ninth and gave up a leadoff double to Matt Chapman, who scored after two groundouts.
Pinch-hitter Dominic Smith singled off the glove of shortstop Casey Schmitt and pinch-runner Jorge Mateo stole second, but Kilian struck out former Giants outfielder Mike Yastrzemski swinging for his sixth save.
With a pair of outstanding pitching performances, San Francisco (35-48) won the last two games of the three-game series against the slumping Braves (49-33), who have dropped six of seven and 12 of 16.
They lead the NL East by three games over surging Philadelphia.