"He has returned to Colorado for further evaluation and to determine treatment plans," US Soccer said in a statement confirming the diagnosis on Sunday.
Howard was hurt while taking a goal kick in a 2-1 qualifying defeat to Mexico on Friday in Columbus, Ohio.
Brad Guzan, who replaced Howard in the 40th minute is expected to get the start against Costa Rica.
US coach Jurgen Klinsmann had already indicated on Friday that Howard was unlikely to travel to Costa Rica.
In confirming the news, US Soccer didn't offer a time frame for Howard's recovery. It could also have MLS Cup playoff implications, with Howard's Colorado Rapids due to face the Seattle Sounders in the Western Conference finals home and away tie later in November.