The Africa Cup of Nations organising committee disqualified Rwanda from the qualifiers for Morocco 2015 on Sunday.
The decision followed a protest made by the Congolese Football Federation regarding the eligibility of Rwandan player, Birori Dady.
Dady had featured in the first leg of the second round qualifier between the two nations last month in Pointe-Noir.
Congo claimed that Dady, who plays for AS Vita Club in Kinshasa, has a different name and age in his passport.
A subsequent Confederation of African Football (Caf) investigation looked at documents provided by the federations of Rwanda, Congo and DR Congo and also heard a testimony from the player on 11 August at Caf headquarters in Cairo.
Whilst the Rwandan FA maintained that to their knowledge the player Dady Birori had one identity, investigations revealed that he was summoned as Etekiama Agiti Tady to join the national team of Rwanda.
Caf established that the player also uses a different age in his passport, and that the two identities referred to a single person.
They have therefore suspended the player until further notice and have banned him from playing for both his club and country.
Rwanda, who beat Congo on penalties over two legs to reach the group phase are disqualified. Congo progress to Group A of qualifying for Morocco 2015 as a replacement for Rwanda where they will meet Nigeria, Sudan and South Africa.
Vincent Nzamwita, the Rwanda FA President confirmed to BBC Sport in Kigali that he had been notified of the news.
“Yes we received communication from Caf about the disqualification.”
He however refused to reveal the next step of action.
Caf say they reserve the right to comment on whether they will impose additional sanctions at the next meeting of the Organising Committee scheduled for 17 September 2014.
African football’s ruling body also urge other “players and stakeholders to regulate the situation of dual identity.”
Caf say the decision takes effect immediately and say that if Rwanda choose to appeal, they will have to do so in accordance with Caf regulations.