Talismanic striker Erling Haaland opened the scoring for Guardiola’s side after just nine minutes after a devastating counterattack.
Arsenal dominated the game from then one, with City being forced to revert to a back five when Phil Foden was replaced by Nathan Ake midway through the second half.
Mikel Arteta’s side piled on the pressure with substitute Gabriel Martinelli finally bagging the equaliser in the 93rd minute.
Speaking after the game, Guardiola admitted his side were already feeling the effects of this season’s hectic schedule.
“They were better and we were incredibly tired,” he said.
“The game against Napoli was so emotional and after that recovery day, but then we have 4-5 hours to travel.
“It’s more fatigue and everything against a team that fought the last two Premier Leagues to win it. Man City spends money. They do as well. We were there. We talk about we have to be super strong in terms of mentality and we had that.”
When pressed on the schedule, Guardiola added: “Of course it’s affects you. We have to be strong. We have a lot of fatigue and missing players.
“John came back. Rayan Cherki, Ait-Nouri. Khusanov was injured. So many things happened. If you want me to complain for the schedule, okay, I am complaining for the schedule (laughing).”