Zabaleta and Bacary Sagna were both dismissed in the last minute of the Emirates Stadium encounter after the pair clashed by the touchline. The Argentina star looked unfortunate at the time and TV replays appeared to back up that view.
So, facing a three-match ban that would rule him out of matches against Leicester, Wolves and Aston Villa, it seems certain City will appeal ahead of the 5pm deadline.
"We are a little bit disappointed with that decision," said assistant manager Brian Kidd.
"We are looking at it and will make a decision about whether to appeal before the deadline. It was very harsh."
Kidd also defended manager Roberto Mancini over the tactics City employed on Wednesday night, claiming the Blues had been forced onto the defensive rather than choosing to play that way.
"I realise this Italian tactics thing gets brought up because the boss is Italian, but I don't understand it," he said.
"We came back from the Emirates with a really good point. Arsenal were terrific for the first 25 minutes but we didn't capitulate when it would have been quite easy to go under."
Kidd could offer no update on the pursuit of Edin Dzeko from Wolfsburg, but it appears only a matter of time before the Bosnian is officially unveiled as a City player. With a fee and personal terms agreed, it is thought the giant striker underwent a medical on Wednesday.
Although he must leave the country pending a work permit being granted, given the player's status as a regular international and one of the most sought-after strikers in Europe, that is regarded as automatic. He would then be clear to complete a deal worth an estimated £27million.