The 32-year-old Gabon forward has left the tournament without kicking a ball.
The Arsenal forward did not feature in either of Gabon’s opening two games at the finals, missing the win over Comoros after contracting coronavirus and then being ruled out of Friday’s draw with Ghana due to a heart concern.
Gabon announced last week that Aubameyang, along with team-mates Mario Lemina and Axel Meye, had been found to have “cardiac lesions”.
The problem was not thought to be serious, but the Gabonese Football Federation has now said Arsenal and Lemina’s club Nice will be able to check on their players.
A statement read: “The Gabon Football Federation decided to make the players Pierre Emerick Aubameyang and Mario Lemina available to their clubs to continue the in-depth examinations.”
Rumours emerged on social media soon after the announcement that Aubameyang and Lemina had contravened disciplinary protocols.
Aubameyang, however, tweeted on Monday evening to dismiss such accusations.
Translated from French, he wrote: “We have problems that are already complicated to solve, then on top of that there are rumours.
“In short, we have health to take care of first and foremost. I won’t go back on these false rumours and I sincerely hope that our team will go as far as possible.”
Midfielder Lemina also took to social media to address the issue, saying on his Instagram Stories: “I’m not even going to feed lies that seek to harm. I have nothing to do (with it).”
Aubameyang, 32, did not feature for Arsenal in the five games leading up to his departure to Cameroon for the Africa Cup of Nations.
He was stripped of the club captaincy and dropped from the first team after returning late from a sanctioned trip abroad – not his first breach of discipline during his time at the Emirates Stadium.
The PA news agency understands Arsenal were in the dark about Aubameyang’s position when Gabon announced his departure and it remains to be seen if he will be back in the first-team picture when he is deemed fit enough to return to action.