The English centre-back was named on team-sheet to face City, but felt tightness in his hamstring which led to him being replaced by David Luiz in the starting XI.
Mikel Arteta convinced Holding to change his mind about leaving the Emirates amid speculation he was set to join Newcastle United on loan in the summer transfer window.
Before Saturday’s match, Holding had started five of Arsenal’s six games in all competitions this season, showcasing the Spanish boss’ increased trust in him.
However, Holding’s progress may now be slightly halted as the Daily Mail claim that his hamstring issue could see him miss the Gunners’ next six games.
Arsenal have a packed schedule up until the next international break in November, with Europa League clashes against Rapid Vienna, Dundalk and Molde, as well as facing Leicester City, Manchester United and Aston Villa in the Premier League.
David Luiz, Gabriel, William Saliba and Sokratis are the remaining natural centre-backs, but the latter hasn’t been included in their squad for the Europa League.