"It was tough," Guardiola told Sky Sports. "But we were compact, we defended high balls well and we played well with the ball in the first half."
Aguero, who missed two penalties in City's 5-0 Champions League playoff victory at Steaua Bucharest on Tuesday, opened the scoring from the spot in the 27th minute after Ryan Shawcross had impeded Nicolas Otamendi.
A Football Association directive before the season instructed referees to be stricter with infringements in the box and City benefited.
"I heard the new rule," Guardiola added. "We have to adjust as referees are so curious about what happens in the box."
Stoke manager Mark Hughes was surprised.
"The decision shocked us, it stopped us in our tracks," he said.
City allowed Stoke back into the match when Shawcross was awarded a penalty after being fouled by Raheem Sterling in the 49th minute and Bojan converted from the spot.
The visitors, not at their best despite dominating possession in the second half, scored again four minutes from time, Iheanacho rounding Given before crossing for Nolito to tap home his first Premier League goal.
Iheanacho was also influential in City's fourth, distracting the Stoke defence with a dummy before Sterling crossed for Nolito to add his second.