Guardiola, who was named among the four nominees for the Premier League’s manager of the month for December on Thursday, will head into a period of self-isolation and will miss City’s FA Cup tie at Swindon Town on Friday.
Guardiola is the sixth Premier League manager to test positive for Coronavirus since December after Steven Gerrard, Patrick Vieira, Mikel Arteta, Jurgen Klopp and Sean Dyche.
Also testing for the virus at the Man City camp are seven unnamed players as well as assistant manager Juanma Lillo.
Rodolfo Borrell, who is one of Guardiola’s assistants, will take charge of the Premier League champions at the County Ground.
A statement issued by City on Thursday read: "Pep Guardiola will miss Friday evening's FA Cup trip to Swindon Town after testing positive for COVID-19.
"The City manager recorded a positive test on Tuesday along with assistant Juanma Lillo. Both are now isolating, along with a number of other positive cases within the City first team bubble.
"This brings the number of those isolating for COVID related reasons amongst the group to 21. Of that number, 14 are backroom staff with seven first team players.
"Assistant coach Rodolfo Borrell will take charge of the team for the trip to Swindon."
