Striker Aubameyang and Gabon teammate Mario Lemina, who plays for French club Nice, both tested positive for Covid-19 on January 6 upon arrival in Cameroon for the ongoing AFCON tournament.
It comes after both players, along with Axel Meyé, who plays for Moroccan club Ittihad Tanger, were ruled out of Gabon's 1-1 draw against Ghana with "heart lesions" detected during medical examinations.
In a statement on Thursday, Gabon's football federation said the pair are being placed at their clubs' disposal "to conduct in-depth exams."
Previously Gabon coach Patrice Neveu had told reporters that the "virus has left some residue on the MRI tests that they underwent."
"Aubameyang and Lemina don't have heart problems, but Covid may have left some waste, so it was wise not to play and we followed the protocols."
Throughout AFCON, CAF, the governing body of football in Africa, is providing players with a medical assessment after contracting Covid-19, which includes a cardiac assessment.
Aubameyang, Lemina and Meyé were all instructed not to play last week's game as CAF "did not want to take risks," according to
Gabon's football federation.
Gabon faces Morocco in its final game of the AFCON group stages on Tuesday as it looks to cement its place in the knockout stages.
Aubameyang previously said he felt physically "fine" after contracting Covid and had returned to training with the rest of the Gabon team.
In December, Arsenal said Aubameyang would no longer be the club's captain following a "disciplinary breach."
The 32-year-old last played for Arsenal in the 2-1 defeat at Everton on December 6.