Guardiola's former assistant Mikel Arteta masterminded a superb 2-0 win for the Gunners, who ended a run of seven consecutive defeats to City thanks to a goal in each half from Pierre Emerick-Aubameyang and a tireless defensive display.
City's underwhelming Premier League campaign will now amble to a conclusion in dead rubbers against Watford and relegated Norwich City over the coming week, with the focus shifting to Real Madrid's visit to Etihad Stadium on 8 August (AEST).
Speaking after the match, Guardiola suggested a two-week break before Zinedine Zidane's LaLiga winners aim to overturn a 2-1 first-leg deficit at the Round of 16 stage would not work in his side's favour.
"Now we have two weeks," Guardiola said. "We wanted to play the [FA Cup] final one week before the Madrid game to be in rhythm.
"We missed this chance."
Even if City makes the most of its advantage over Madrid, the prospects of it coming through next month's mini-tournament of one-off games in Lisbon next month would feel remote given its record against high-class opponents this season.
Arsenal joined Liverpool, Chelsea, Tottenham Hotspur, Wolverhampton Wanderers (twice) and Manchester United (three times) in recording victories over the 2018-2019 domestic treble winner and Guardiola did not spare his players.
"We didn’t play good," he said. "The only regret is we didn't play in the first half like we did in the second."
Raheem Sterling, Kevin De Bruyne and Riyad Mahrez all went close for City after half-time, although the latter's 54th-minute strike proved to be its only attempt on target.
"On the day when you have to play good, we didn't," Guardiola added.
"We started slow and without the way you have to play these kind of games. We've done it many times. We were ready, but today we did not do it.
"We were not good. In these games you have to be good to go through."