Halladay (10-7) allowed five hits and struck out seven to record his second straight complete game. The All-Star right-hander outdueled Derek Lowe (9-7) and needed just 93 pitches to finish.
Chipper Jones homered for the NL East-leading Braves.
The two-time NL champion Phillies, who lost three of four to lowly Pittsburgh over the weekend, need to win this three-game series to avoid losing more ground in the division. They're 17-23 in the last 40 games and trail Atlanta by four games.
