The 22-year-old is isolating after contracting the virus and misses the New Year’s Day clash along with his manager Mikel Arteta, who has tested positive for Covid for the second time.
He is also set to be absent for the midweek League Cup semi-final game against Liverpool at the Emirates stadium.
Eddie Nketiah has tested positive for Covid-19 and misses Arsenal v Manchester City
Calum Chambers, Cedric Soares, Takehiro Tomiyasu and Ainsley Maitland-Niles have all tested positive in recent weeks at the Gunners.
Nketiah has only played six times for Arsenal in all competitions so far this season but recently scored a hat-trick in the 5-1 League Cup victory over Sunderland on December 21.
Arsenal head into Saturday’s clash against league leaders City looking to consolidate their place in the top four of the Premier League standings.
Arteta’s side are four points clear of nearest contenders West Ham but there is a big chasing pack for the final Champions League place.
Manchester United have a game in hand on Arsenal and rivals Tottenham, who face Watford later on Saturday, have two after Covid-19 postponements.
Mikel Arteta is absent from the match with City after testing positive for the second time