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The City boss has been careful with Aguero's recovery following his operation in June after a hamstring injury at West Ham curtailed his initial return in October.
"Unfortunately he was in contact more than usual with one person who is positive," Guardiola confirmed after the game. "He must isolate for a few days. I don't know exactly because he has been tested like all of us six times in the last 10 to15 days so it is negative.
"Today, I think he was negative too but the protocols say in some cases isolate, and in other cases we still play football. He was not able to play today."
Guardiola was able to start with Gabriel Jesus and Kyle Walker for the first time since they tested positive for Covid-19 on Christmas Day.
City are close to havinga full squad available after the coronavirus outbreak at the club that forced the game against Everton on December 28 to be called off at short notice.
Ederson, Ferran Torres and Tommy Doyle have also returned to first-team training after positive tests and could be in contention for Wednesday's Premier League clash with Brighton at Etihad Stadium.
Aymeric Laporte missed the game with a minor hamstring injury, but Guardiola hopes to have him back soon.
"Laporte yesterday had a first session alone," he said. "So hopefully in one week, I don't know exactly but hopefully one week, ten days he will be OK."
City progressed comfortably with two goals from Bernardo Silva and a third from Phil Foden while academy yoingsters Felix Nmecha, Taylor Harwood-Bellis and Liam Delap got valuable game time in the second half.
"Our first objective is done. Some young players were involved and we have qualified for the next round," Guardiola added."If you follow the trajectory of our team since I arrived, we didn't drop one game. That's why we are in a fourth Carabao Cup final in a row, the FA Cup we won two seasons ago, and a semi-final last season.
"Players like Kyle and Gabriel came back. Rodri didn't play last game, Mendy for a long time didn't play. So for six, seven players today was good.