The Phillies scored a run in the bottom of the ninth and had two runners on before Kenley Jansen finally recorded the final out of the contest.
Los Angeles won its third in a row and the Phillies have suffered five straight setbacks.
A bases-loaded walk to Loney in the ninth gave the Dodgers a two-run lead, which they needed to fight off the Phillies in the bottom half of the inning.
Jansen hit a batter, threw a wild pitch and gave up an RBI double to Ty Wigginton that brought the Phillies within one. Philadelphia had runners on first and second when Jansen got Brian Schneider on a popup to end the game.
It was Jansen's ninth save and he preserved the win for Chris Capuano (8-2), who allowed four runs on four hits in five innings.