The Central African nation claimed a 3-1 aggregate victory over Mauritania in the first round of qualifying, but had been under investigation since their opponents questioned the eligibility of attacker Thierry Fidjeu Tazemeta.
The 31-year-old was by no means a newcomer to the side, having featured for them at the 2012 tournament on home soil, but CAF confirmed on Thursday that the country will be removed from qualifying for next year's event.
Tweeting their judgement, CAF said: "Organising committee of AFCON disqualified Equatorial Guinea from the play-offs of AFCON Morocco 2015 in a decision reached 3rd July 2014.
"AFCON organising committee decision to disqualify Equatorial Guinea follows protest brought by Mauritania Football Federation.
"Mauritania protested fielding of Thierry Fidjeu Tazemeta in first round play-off of 17th May 2014 Mauritania and Equatorial Guinea played in Nouakchott.
"Of Cameroonian origin, Thierry Fidjeu Tazemeta, was born 13 Oct 1982 in Mbouda, according to Federation of Cameroonian Football.
"Equatorial Guinea didn't provide evidence Tazemeta was eligible to represent them or complied with FIFA Statutes on change of association.
"Consequently, Mauritania is qualified to next play-off round of #AFCON 2015 and national team of Equatorial Guinea is deemed to be 'eliminated'.
"Mauritanian now proceed to engage Uganda in final playoff round with 1st leg on 19 July in Kampala to kick off at 16:00 local time."
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