Nigeria keeper Vincent Enyeama
The 28-year-old Nigerian player of the year had wanted to play but his Israeli club Hapoel Tel Aviv preferred he did not.
"Enyeama told head coach, Samson Siasia, that he has an ankle injury which he has been treating with pain killers, but his Israeli club Hapoel Tel Aviv have now ordered him to rest," said Ademola Olajire, spokesman for the Nigeria Football Federation (NFF).
Enyeama has been the country's first choice goalkeeper since the 2002 World Cup and was outstanding at last year's World Cup finals in South Africa.
In his absence, another Israel-based goalkeeper, Dele Aiyenugba, will most likely be in goal against Ethiopia on Sunday in Abuja.
Siasia has also called up goalkeeper Sunday Rotimi from Dolphin of Port Harcourt, who are top of the Nigeria Premier League.
Nigeria began training for the Group B match on Monday in Abuja with the bulk of the foreign-based professionals led by England-based strikers Obafemi Martins and Osaze Odemwingie expected to arrive on Tuesday.
The Super Eagles are second behind Guinea with three points from two matches.
Ethiopia are third on three points, while Madagascar are yet to record a point.
The overall winners of this group will earn an automatic ticket to next year's Nations Cup to be co-hosted by Gabon and Equatorial Guinea.
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