Rwanda looked set to feature in the final group phase of qualification for the continental showpiece after beating Congo on penalties in a two-legged tie earlier this month.
However, Stephen Constantine's men were duly thrown out of the competition following a protest from the Congolese Football Federation (FECOFOOT).
The sanction surrounded the eligibility of Rwanda's Birori Dady, who was found to be playing for Vita Club with a passport for the Democratic Republic of Congo under the name Etekiama Agiti Tady and with a different age.
Rwanda had appealed the decision in the hope of being allowed to re-enter the competition but on Saturday, the CAF confirmed their initial verdict would not be overturned.
"The appeals board of CAF has upheld the decision of the organising committee of the Africa Cup of Nations, which disqualified Rwanda from the final group phase of qualifying for AFCON Morocco 2015," read a statement from the governing body.
"Congo is therefore qualified for the last phase of qualification for the Orange AFCON Morocco 2015 and will compete in Group A against Nigeria, South Africa and Sudan in place of Rwanda.
"It was established that the player Dady Birori, playing with the national team of Rwanda, was the same that played in the Champions League with the club AS Vita using the name Etekiama Agiti Tady.
"Based on the documents on record, it was evident that the Rwandan federation was aware of this double identity but proceeded to feature the player for the national team while he held a different identity with the club."
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