City will be hit with an FA charge of failing to control their fans, following the pitch invasion at the final whistle at the Etihad Stadium.
Stewards and police were powerless to stop the fans - at least one letting off a flare - from spilling on to the pitch in City's first game since clinching the title.
But Guardiola leapt to the defence of City fans and said they had every right to celebrate their club's title triumph by showing their emotions.
“Football is an emotional game," said Guardiola. "I understand you have to be careful, but they feel they want to share that they are happy.
“It's better they stay where they should stay, but I'm not going to tell them 'don't do that'. If they are happy, I like to be close with them.
“They show how happy they are and that's the most beautiful thing. We felt that today. The fans here were so happy.
“Just arriving on the bus, the way people look at us and celebrate in the stadium and jump. I'm sorry, that's good.
“It's time to celebrate it. I'm not going to tell anybody 'don't enjoy it'. I'm not going to tell them.
"But save the grass - we need the pitch for the future.