The 34-year-old was missing from the bench when the Bavarians demolished Benfica 4-0 away from home in the UEFA Champions League on Wednesday.
Assistant managers Dino Toppmoller and Xaver Zembrod oversaw proceedings from the bench as Leroy Sane's brace, Robert Lewandowski and an own goal from Everton gave Bayern Munich their third straight win in Europe's Premier club competition this season and they are yet to concede a single goal.
"Julian Nagelsmann, 34, head coach of FC Bayern Munich, tested positive for the corona virus despite being completely vaccinated," Bayern have said in a statement on the club's official website.
"He will return to Munich separately from the team in a medical plane and will go into domestic isolation."
Nagelsmann will have to isolate, meaning he will not be on the touchline for Saturday's Bundesliga game against TSG Hoffenheim.
Toppmoller said afterwards: "It was a lot of fun in an unfamiliar role. The boys did sensationally well - especially in the second half. A great performance. We had a lot of chances."
Nagelsmann was appointed Bayern Munich manager on a five-year contract in the summer, replacing Hansi Flick in the role, and has won 11 of his 13 competitive games in charge.
Bayern Munich are top of the Bundesliga table, one point clear of Bayern Munich in second and are five points ahead of Benfica in their Champions League group.