City will be without the striker for their trip to Stamford Bridge on Saturday.
It came after the Argentina forward was a passenger in a taxi that crashed on its way to the airport in Amsterdam on Thursday night.
Aguero, 29, had been to a concert in the Dutch capital on his day off and suffered a broken rib in the smash, when the driver lost control of the vehicle on a bend and it struck a post.
There have been question marks over why Aguero was abroad just 48 hours before his side’s top-of-the-table clash with Chelsea.
In a statement, City said Aguero was in the Netherlands “on his day off” - and Guardiola reiterated that the forward had done nothing wrong.
Guardiola said: “It was his day off. I am not the police.
“I think days off are for players to be happy. I want the players to be happy.
“I don’t like to train everyday because I think players need to rest mentally and physically, and they can enjoy their lives.
“I want my players to have fun. So he decided to go there, it’s ok for me.”
The manager confirmed he isn’t going to impose more rules on his squad, to make them stay at home on their days off.
He said: “We have enough rules. Play right, play left, defend the long balls, set pieces, control the counter attack from [Eden] Hazard, Pedro, Willian,” he joked. “We have enough rules.
“I will speak to him this afternoon to ask how he is, but I know he’s ok.
“It was an accident and you’re always worried about what happened, but he’s ok and that is the most important thing.
“After that, he will recover as soon as possible.
“He cannot play tomorrow and after the international break - maybe he was selected for Argentina, but he cannot go there.
“We will see. I don’t know the assessment of the doctor. The first impression that we have is that he has a broken rib, but exactly how many days he’ll be off I don’t know right now.”
Aguero has scored six times in his last five games for the club, including an impressive hat-trick at Watford.
The Argentine is one goal away from equalling Manchester City’s club scoring record of 177, set by Eric Brook in the 1930s - but he’ll now have to wait to pass that tally.
