Referee Michael Oliver had to bring the silence to a premature end as chanting from the City end of Wembley marred the marking of the 33rd anniversary of the disaster.
The club released a statement on the incident, apologising to Liverpool for the actions of those fans, and Guardiola has echoed that sentiment as he criticised those involved.
“I think Manchester City made a statement,” Guardiola said.
“This is not Manchester City. We are close to Liverpool club for the tragedy that happened years ago. We are alongside them.
“After these guys singing (it) doesn’t represent what we are.”
On the pitch it was just as painful an afternoon for City, as they saw their treble hopes come to an end after a 3-2 defeat.
Guardiola’s side were 3-0 down at the break, the second of those goals coming as Sadio Mane slid in and caught goalkeeper Zack Steffen taking far 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 an error can occur with the team’s style of play.
“It was an accident,” Guardiola said.
“One of the strong points is try to play [out] and as a keeper he has this 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 have spoken with the team – not him personally but he is strong.”