The Arsenal midfielder is on loan at Hertha and captained France’s age-group side to a 5-0 win over Liechtenstein on Thursday and a 1-0 victory over Slovakia on Monday.
Hertha announced that Guendouzi was tested on Tuesday and again on Wednesday with both results coming back positive.
He will sit out a 10-day quarantine period that will prevent him from making his debut for Hertha against Stuttgart in the Bundesliga on Saturday.
In a statement, the club wrote: ‘Matteo Guendouzi has tested positive for Covid-19 after returning from international duty.
‘There has been no contact with any Hertha players or staff. He is symptom-free and feeling well, but will now self-isolate for 10 days.
‘Get well soon, Matteo!’
Guendouzi started life at Arsenal impressively and became a regular starter in the side but his progress unravelled after the restart last season.
He has been persona non grata at the Emirates since their 2-1 defeat against Brighton in June, where he was involved in a post-match scuffle with Neal Maupay.
After leaving on the season-long loan, he said: ‘I just really needed to play this year, a new challenge.
‘That was the most important thing for me. I am still young, I am only 21, so playing time was the top priority for me.
‘So Hertha Berlin, I know that I will be able to express myself in a magnificent league.’