Referee Stuart Attwell initially indicated an additional eight minutes at the end of the game, but it was extended further due to a clash of heads in that period involving Kyle Walker and Thomas Partey.
In an effort to clamp down on time-wasting, referees have been instructed to add on more time for any in-game delays, but Guardiola said the alterations could have a profound effect on matches.
"It is not annoying, we have to get used to it," Guardiola said. "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 [rule-making International Football Association Board] 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. Now the games 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 9 a.m. I am here playing."
Gunners boss Mikel Arteta also said some of the new rules can be frustrating after he was booked for gesturing for a yellow card -- another clampdown from officials as part of a new technical area code of conduct.
"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."