A disappointing day for the Gunners was capped off when the former Real Madrid player was told off by his team-mate for not showing his appreciation to the supporters
Instead of acknowledging his side's travelling support, Ozil headed straight for the tunnel but Mertesacker, who had gone over to the away section, argued with his countryman.
Arsenal manager Arsene Wenger played down the incident between the pair after the match: "That is the Germans, they will sort that out between themselves. Don't worry."
Sergio Aguero opened the scoring before Theo Walcott pulled the Gunners level. Alvaro Negredo's goal ensured City went into the break with a lead, while a double from Fernandinho, along with a goal from David Silva and a Yaya Toure penalty secured the win for Manuel Pellegrini's side.
City are now three points behind Premier League leaders Arsenal after 16 games played.
Arsenal's day was made even worse after defender Laurent Koscielny suffered a deep cut to his knee in the first half and needed to be stretchered off.