Retiring Northern Ireland captain Hughes is not fit to play against Estonia and Italy.
The defender recently announced his decision to quit international football when the current European campaign concludes and an untimely injury has now brought about a premature end to his NI career.
The 31-year-old had hoped to lead the side out for the final time at Windsor Park against Estonia on Friday before making his last appearance against Italy four days later but instead finishes up with 79 caps, having made his debut in 1998.
The Fulham defender hopes to prolong his top-flight career for as long as possible and last week decided his country's arduous World Cup 2014 qualification schedule - which includes trips to Russia, Azerbaijan and Israel - would be a campaign too far.
Hughes enjoyed a distinguished international career after debuting against Slovakia in 1998 and scored his first and only goal against the Faroe Islands in August.
On a difficult day for boss Nigel Worthington, Hughes was joined by striker Josh McQuoid (virus) and midfielder Jamie Ward (hamstring) in pulling out of both games.
Manchester United defender Jonny Evans is doubtful for the fixtures with an ankle problem while Preston defender Conor McLaughlin has been called up as cover.