Referee Michael Oliver had to end the silence prematurely as chants from the Wembley Town side marked the 33rd anniversary of the disaster.
The club issued a statement about the incident, apologizing to Liverpool for the actions of those fans, and Guardiola echoed that sentiment by criticizing those involved.
“I think Manchester City have made a statement,” Guardiola said.
“It’s not Manchester City. We are close to the Liverpool club for the tragedy that happened years ago. We are on their side.
“After these guys sing (it) doesn’t represent who we are.”
On the pitch, the afternoon was equally painful for City, who saw their hat-tricks come to an end after a 3-2 defeat.
Guardiola’s side trailed 3-0 at the break, with the second of those goals coming when Sadio Mane slipped in and caught goalkeeper Zack Steffen taking way too long on the ball.
The City boss made the decision to start Steffen instead of Ederson at Wembley, as he often does in domestic cup competitions, and accepted that such a mistake could happen with the style of play of the team.
“It was an accident,” Guardiola said.
“One of the strengths is trying to play [out] and as a goalkeeper he has that quality. It was an accident and he will learn for the future. When the ball is there, it can always happen. It was an accident and he will learn for the future.
“I spoke with the team – not him personally but he is strong.”