Anouma took his case to CAS after the Confederation of African Football judged he could not stand against long-time incumbent Issa Hayatou as he was not and had never been a member of the CAF Executive Committee - a condition of the CAF Statutes imposed by Hayatou in September.
He had been proposed for the position by the Ivorian Football Federation (FIF).
Cameroonian Hayatou will now stand unopposed at the CAF congress at its congress in Marrakech this weekend.
A CAS statement read: "The CAS Panel in charge of the case, after having heard the parties at a hearing on 1 February 2013, decided to dismiss the appeal of Jacques Anouma; broadly following the reasoning of the CAF Executive Committee, whose jurisdiction to decide the contested decision was recognised by the CAS.
"Thus, it was confirmed that the CAF Statutes adopted in September 2012 were applicable in assessing the validity of the candidates in the presidential election and Anouma did not meet these criteria because he had never been a member the CAF Executive Committee.
"The CAS, however, recognised Jacques Anouma's right to appeal alone to the CAS despite the fact that his candidacy had been put forward by the FIF and that such Federation did not support Anouma during the arbitration procedure."