Halladay informed the team on Wednesday night after his start. Halladay is expected to rejoin the team in Washington, D.C. on Friday.
His next scheduled start is Monday night in Philadelphia.
This comes after Halladay struggled in a 11 inning game against the Braves in Atlanta on Wednesday night.
Halladay gave up eight runs to blow a six-run lead as the Phils lost 15-13.
After the game, Halladay offered regret for his teammates, especially Carlos Ruiz, instead of excuses for himself after his worst outing in five years.
Ruiz had three hits, including a three-run homer in the seventh and a three-run double in the eighth.
"He's been awesome for us," said Halladay of Ruiz. "I think that's what hurts most. When you have games like this, your teammates are out there grinding and getting it done and I didn't. And that was the difference, really.
"That's the toughest one, letting those guys down who really got it done today."
Halladay gave up 12 hits - one below his career high - and eight runs in 5 1-3 innings.
Halladay was tagged by Brian McCann's fifth career slam in the fifth. The former Cy Young winner had not allowed as many earned runs since May 5, 2007, when he gave up nine runs in 5 1-3 innings at Texas.
"Honestly, I felt good," Halladay said after seeing his ERA climb from 1.95 to 3.40. "There were some that I didn't execute. It wasn't anything else."
Meanwhile, Phillies LHP Cliff Lee, on the 15-day disabled list with a strained left oblique muscle, threw in the bullpen before the game. If he has no discomfort, he plans another bullpen session on Saturday. If all goes well on Saturday, Lee is expected to come off the disabled list.