The Teranga Lions are due to start their Group B campaign against Zimbabwe in Bafoussam on Monday.
"Kalidou Koulibaly has tested positive for Covid-19 while on international duty with Senegal. The defender, who is vaccinated and asymptomatic, is now in self-isolation as per protocol," a Napoli statement said.
Senegal, Africa's top-ranked team, delayed their departure for the tournament by a day earlier this week after three players and six staff members returned positive tests.
The squad left without the three players who were placed in quarantine.
CAF has said teams will have to play their matches even if they only have 11 players available. An outfield player must go in goal if there is no recognised goalkeeper.
Any team that is unable to fulfil a fixture will forfeit the match 2-0.
African football officials said in "exceptional cases" the tournament organisers "will take the appropriate decision".
