Choupo-Moting had already been self-isolating, along with team-mates Serge Gnabry, Joshua Kimmich, Jamal Musiala and Michael Cuisance, after coming into contact with a person who had contracted the respiratory illness.
Bundesliga leaders Bayern confirmed on their official website on Wednesday that the 32-year-old has also now tested positive and will continue to quarantine.
"Eric Maxim Choupo-Moting has tested positive for COVID-19," the statement read.
"The FC Bayern forward is self-isolating at home in accordance with the relevant health authorities and doing well under the circumstances."
German media outlet Bild reported last week that Bayern has told players it will have its pay withheld for time missed in quarantine if they have not been fully vaccinated.
Choupo-Moting, who has made 11 of his 12 appearances for the German champion this season from the bench, is reported to be among those yet to receive both doses.
However, speaking on Monday, head coach Julian Nagelsmann insisted he does not see the issue of players potentially going unpaid causing any friction in the camp.
"It's always a group's distinction that you don't always agree," he said.
"In a functioning team, however, everyone has to be there for everyone. I don't think it will break the team, we have to grow from it.
"By not vaccinating, they are more likely to fail. But we have to be there for each other, we should grow from that.
"You often have conversations, if the person is positive, you have to be in quarantine as an unvaccinated person.
"The players are doing fine though, they are being tested. Josh could return earlier than the others because he was quarantined earlier."
In better news for Bayern, Niklas Sule and Josip Stanisic returned to individual training on Wednesday after completing their own periods of self-isolation.
Dayot Upamecano also took part in training a day on from missing Bayern's 2-1 Champions League win at Dynamo Kiev that clinched top spot in Group E.