The Belgium playmaker is now isolating and will miss the games against Everton and Paris St Germain.
De Bruyne returned the positive test some time after Belgium’s draw with Wales in World Cup qualifying on Tuesday, a match in which he scored.
City manager Pep Guardiola said: “Unfortunately Kevin got positive from Covid in Belgium. He will be 10 days isolating. Two days ago he told me.
“I think he’s here in England but forget about his fitness and momentum – he’s positive and has to recover well, be healthy as possible. That’s more important than everything else.
“When someone is positive be careful because people are still dying right now in this pandemic situation.
“He was vaccinated so he’s more protected and hopefully the symptoms will be minor.”
Fellow midfielder Jack Grealish could also miss the game at Goodison Park with the knock that forced him to pull out of the England squad for Monday’s World Cup qualifier in San Marino.
Phil Foden also picked up a problem but has a better chance of featuring at the weekend.
Guardiola said at his pre-match press conference: “Jack is getting better, Phil Foden came back with a problem in his leg.
“Jack I don’t think (will be available), Phil maybe.”