Flyers general manager Paul Holmgren made the announcement on Tuesday.
Jagr, 39, is in his first season with Philadelphia after three in Russia, and was one of this summer's marquee free agents. The former Penguin, Capital and Ranger played only a minute of the second period at Citizens Bank Park in the Flyers' 3-2 loss to the Rangers. He was replaced on Philadelphia's top line by James van Riemsdyk.
Jagr has 12 goals, 31 points and is a plus-12 for the Flyers, who now trail the first-place Rangers by four points in the Atlantic Division. Philadelphia plays host to Chicago on Thursday at the Wells Fargo Center.
Jagr left the ice in the first period and walked down the long runway to the Phillies dugout, only to return in the second before making it through just one shift.
Flyers coach Peter Laviolette, in the Winter Classic postgame, deferred all questioning to Holmgren with regards to Jagr.
"He updates all of the injuries," Laviolette said. "I didn't bench him."
Jagr's injury comes at an inopportune time. The Flyers are still comfortably in the Eastern Conference playoff mix -- they would have been the No. 4 seed if the season ended Monday night -- but they were only five points away from the No. 8 seed, and have allowed 109 goals with the surging Blackhawks on deck.
The loss to the Rangers was the third this season for Philadelphia.
"The last two games I thought we were better, and results have not gone our way," Laviolette said of the Rangers. "We will continue to look at it and continue to work at it. They are an opponent that is, I think, somebody that we'll have to deal with in the future. They have got a good hockey team that played well to this point, and in saying that, the last two games, I think we are taking strides, and what's next is the scoreboard. That's where we have to get them."
It doesn't help matters that the Flyers are now smack dab in the middle of a goaltending controversy. Ilya Bryzgalov (14 wins and a 3.01 goals-against average), an All-Star acquired from Phoenix in the summer to secure a shaky situation in net, did not start the Winter Classic, leaving the door open for second-year netminder Sergei Bobrovsky (8 wins, 2.56), who could not hold a 2-0 lead against New York in the outside conditions.
And all of it, of course, was captured up close and personal by HBO's cameras for the four-week reality series, "24/7."
"Yeah," Laviolette said, "we are all ready to say goodbye to HBO."