Aguero had been in isolation after coming into close contact with someone who had tested positive for COVID-19 and missed City's last three matches against Brighton & Hove Albion, Crystal Palace and Aston Villa.
But, despite his self-isolation, Aguero tweeted on Thursday that results of a recent test have shown he is positive for the virus.
"After a close contact, I've been self-isolating and the latest test I took was positive for COVID-19," he posted on Twitter.
"I had some symptoms and I'm following doctor's orders for recovery. Take care, everyone!"
Aguero will now need to self-isolate for 10 days for his positive test but needs a negative result before he can play for the club again.
The news is a blow to both City, who are sweating on the fitness of midfielder Kevin De Bruyne and Kyle Walker, and Aguero as the injuries have restricted the Argentina forward to just five Premier League appearances this season.
City have seen an increase in coronavirus positives within the club since Christmas, with five players self-isolating in early January.
Liverpool and City have been the top two sides in the Premier League each of the last two seasons -- with Pep Guardiola's side missing out on the title last term.
City have won their last six league matches and sit second in the table. They are two points behind leaders Manchester United with a game in hand.