Nowak will head Philadelphia Union's soccer operations as team manager when it begins play next year.
Philadelphia Union CEO Nick Sakiewicz says Nowak was the coach the expansion team targeted from the start.
Nowak, a former Polish national team captain, won MLS titles as a player and coach. He was a member of the Chicago Fire team that won the MLS Cup in 1998 and was the head coach of D.C. United's 2004 championship team.
U.S. Soccer announced Nowak's departure from the national team on Thursday. Nowak had served as the top assistant on the men's team and led the under-23 national team at the 2008 Beijing Olympics.
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