Halladay allowed one hit and a walk. He was sweating profusely when he was pitching and at one point bent over behind the mound.
The two-time Cy Young Award winner was roughed up in his previous start and said he felt "lethargic" afterward. He insisted he had no injury. Halladay missed almost two months last year with a shoulder problem.
Zach Miner took over for Halladay in the second inning and allowed one run on four hits in two innings.
Freddy Galvis hit a two-run homer for the Phillies - homering on St. Patrick's Day for the third straight year.