Snyder matched his career high with five RBI, including the grand slam off Buddy Carlyle in a six-run ninth.
Rookie Gerardo Parra drove in three runs with three hits as Arizona ended a four-game losing streak.
Scherzer (1-3) gave up four hits and three walks with four strikeouts.
Braves relievers walked eight batters in four innings. Jeff Bennett and Carlyle forced in runs with bases-loaded walks in the eighth and ninth innings, respectively.
Scherzer's first win came in his 14th start. He lost his first seven decisions over two seasons and entered the game with a career 3.39 ERA in 22 games.
Poor baserunning hurt the Braves after Yunel Escobar and Chipper Jones hit one-out singles in the first inning.
With runners on first and third, Scherzer's pickoff throw to first caught Jones breaking to second. Shortstop Stephen Drew tagged Jones to end a brief rundown, and Drew threw to third where Mark Reynolds put the tag on Escobar trying to dive back to the bag.
Kenshin Kawakami (2-5) gave up five hits and three runs in five innings.
He retired the last eight batters he faced before he was removed for a pinch hitter.
Four of Arizona's five hits off Kawakami were extra-base hits, including back-to-back doubles by Reynolds and Eric Byrnes that gave the Diamondbacks a 1-0 lead in the second. Byrnes scored later in the inning on Snyder's sacrifice fly.
Kawakami has lost five of his past six starts and has not lasted more than six innings in any of his seven starts.
Atlanta reliever James Parr walked Chad Tracy and Snyder to start the seventh, setting up a two-run triple by Parra.
The control problems continued in the eighth, when Bennett walked four batters, including a bases-loaded pass to pinch-hitter Miguel Montero to force in a run.
Carlyle added two walks in the ninth. Byrnes had a run-scoring single before Snyder's grand slam over the center-field wall.
TAKING TIME: More than a week after his return from the disabled list, Brian McCann says his adjustment to playing with glasses continues.
"I'm getting there," McCann said before Saturday's game.
McCann missed 13 games due to blurred vision in his left eye. He couldn't play with contact lenses and finally made his return on May 8 after being fitted with new sports glasses.
McCann had laser surgery on his eyes after the 2007 season.
He said the procedure changed the shape of his eyes, making contacts more difficult to wear.