The Arsenal striker tested positive for Covid-19 on arrival in Cameroon last week but subsequently posted on social media to say he had made a full recovery.
However, Gabon announced that Aubameyang, along with team-mates Mario Lemina and Axel Meye, had all been left out due to “cardiac lesions”.
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Arsenal are understood to be satisfied that Aubameyang’s condition is not serious.
The Gabonese Football Federation said in a statement: “According to the CAF medical commission, the players Pierre-Emerick Aubameyang, Axel Meye and Mario Lemina, barely out of Covid, cannot take part in this match.
“An examination showed cardiac lesions, and CAF did not want to take any risks.”