Ryan Ludwick and Jay Bruce both went 2-4 with an RBI, while Bronson Arroyo went eight innings strong, giving up just three hits on 86 pitches.
Aroldis Chapman picked up his 31st save of the season, holding off the middle of the Phillies batting order in the bottom of the ninth to secure victory.
Despite a quality start from Vance Worley, who gave up two earned runs over six innings, the team's offense was unable to pick up their starting pitcher, as the loss keeps the Phillies in the NL East basement at 57-67. The team has lost five of their last 10 games.
The two teams will wrap up their four-game series Thursday as Cole Hamels (14-6) will face NL Cy Young candidate Johnny Cueto (16-6).
The Phillies will look for a split before welcoming the division-leading Washington Nationals for a weekend series.