Moses had been recalled for the Group A matches in Khartoum on Saturday and Abuja next Wednesday after being dropped from the squad following the World Cup.
However, the 23-year-old was injured playing for Stoke City against Sunderland on Saturday, withdrawn after just 18 minutes of the Premier League fixture.
Nigeria coach Stephen Keshi has named Edem Eduok of Dolphins as his replacement.
The Super Eagles, who are reigning continental champions, have just one point from their opening two qualifying matches for the 2015 finals in Morocco.
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(Reporting by Mark Gleeson in Cape Town; Editing by John O'Brien)
