A groin injury forced the retiring Northern Ireland captain out of his side's final Euro 2012 qualifiers against Estonia and Italy.
Hughes announced his decision to call time on his international career last month but was hoping to lead his country out for a final time at Windsor Park on Friday before a high-profile final appearance against the Azzurri four days later.
But the 31-year-old was forced off after 20 minutes of Fulham's Barclays Premier League match against Blackburn on September 11 and has not played since.
Hughes made 193 appearances for Newcastle between 1997/2005 making his debut at the famous Barcelona Nou Camp.