Pinch-hitter Brooks Conrad bounced a one-out double over the right-field corner fence in the deciding frame. A groundout moved him to third before Giants reliever Javier Lopez (5-2) gave up Prado's base hit through the right side of the infield.
Atlanta notched its second consecutive walk-off win after opening this four- game series Monday by rallying with three runs against Brian Wilson in the ninth. Arodys Vizcaino (1-0) was the beneficiary of Tuesday's heroics.
The Braves lead the majors with 22 wins in their final at-bat this season.