Nick Markakis homered for the Braves, who snapped an 11-game skid in Denver.
The game was tied in the eighth when Phillips reached on a one-out double off Pat Neshek (3-3). One out later Tyler Flowers hit a routine grounder to Arenado at third base, but his throw to first was off line and skipped away from Mark Reynolds, allowing Phillips to score from second.
Arenado, who has won the Gold Glove at third in each of his four seasons, has five errors in 306 total chances this season.
Sam Freeman (2-0) pitched the seventh and Arodys Vizcaino worked the ninth for his seventh save.
The Rockies remained tied with Arizona for the NL's second wild card.
