Cole Palmer’s 77th-minute strike looked like it would be enough for City to win the trophy.
But Leandro Trossard equalised 11 minutes into injury-time and Arsenal went on to win on penalties.
There were originally eight minutes of added time but that was extended after a clash of heads between Kyle Walker and Thomas Partey.
“It is not annoying, we have to get used to it,” said City boss Guardiola.
“I had the feeling, not because we were winning 1-0, it was just the fact I had a feeling that much didn’t happen to extend by eight minutes.
“But it is a good question for the International Board [the International Football Association Board who instructed the rule change] and all the people because they don’t consult the managers, they don’t consult the players.
“What is their opinion, we have to accept it and we have to do it.
“Now the games will not be 90 minutes, they will be 100 minutes, that’s for sure. It never happened today and it was eight minutes, imagine if they extend for goals and every time you score a goal in a game [that is] 4-3. You put 30 seconds, 45 seconds on for seven goals, tomorrow morning at 9am I am here playing.”
Arsenal boss Mikel Arteta also fell foul of a new rule aimed at clamping down on dissent.
Arteta waved an imaginary card as he gestured that Rodri should have been booked for a foul on Kai Havertz.
The act was not seen favourably by referee Stuart Attwell, who showed Arteta a yellow card for his actions.
“I just said, ‘I cannot change my behaviour in three days,”‘ Arteta said.
“It’s a very difficult thing to do and I understand that next time we cannot say tomorrow we play with no offsides and then the next time the linesman says, ‘Oh what is he doing?’
“We try our best, I try my best. I understand the rules and where they’re coming from. Sometimes we get frustrated there because we don’t know in what part of the technical area we are. It’s fine. We’ll adapt.”
Asked about the added time, Arteta added: “At the end, it’s about effective time.
“I think it’s really good to do that, because it was going too far I think and now teams are going to have to think twice.
“Now we have to be prepared to play 100 minutes because it’s going to happen every single week.”
Both sides will now turn their attentions to the start of the Premier League season next weekend.
Cole Palmer of Manchester City celebrates after scoring
Image credit: Getty Images
City open the campaign when they face newly-promoted Burnley on Friday. They then play Sevilla in the Super Cup next week before facing Newcastle.
“Win or lose, right now I know the position of the team,” said Guardiola.
“We have to recover well and prepare for Burnley and then travel to Athens, play at 10pm, finish at 2am come back and play Saturday against Newcastle at home. This is my plan.
“We would love to win today absolutely but sometimes you have to accept it and give credit to your opponent.”
Arsenal play Nottingham Forest in their opening game on Saturday, August 12, live on TNT Sports.
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