Stephen Constantine's men made sure of a place in the group stages of qualification by beating Congo on penalties on earlier this month after coming back from a 2-0 first-leg deficit.
However, Rwanda have now been thrown out of the competition by the Confederation of African Football (CAF) following a protest from the Congolese Football Federation (FECOFOOT) during the first leg on July 20.
Congo's appeal surrounded the eligibility of Rwanda's Birori Dady, who was found to be playing for club side Vita Club with a passport for the Democratic Republic of Congo under the name Etekiama Agiti Tady and with a different age.
A CAF statement read: "Following investigations by CAF and on the basis of documents provided by the federations of Rwanda, Congo and DR Congo, and hearing the player's testimony on 11 August 2014 at CAF headquarters in Cairo, CAF established that the two identities only referred to a single person.
"While the Rwandan Football Federation (FERWAFA) maintained that to their knowledge the player Dady Birori had one identity, investigations revealed that he was summoned as Etekiama Agiti Tady by FERWAFA to join the national team of Rwanda."
As a result Congo have now been declared as the winners of the second-round tie and move into the group stages of qualification, where they will take on Nigeria, South Africa and Sudan.
Meanwhile, Dady has been suspended from club and national duty until further notice, with the exact length of his ban to be confirmed at a meeting of CAF organising committee.
