The Barcelona striker has been ruled out of action for three months after suffering the effects of a cardiovascular concern.
Aguero was taken off on the cusp of half-time in Barcelona’s 1-1 draw with Deportivo Alaves at the Camp Nou on Saturday after complaining of chest pains.
"I sent a message to him through his agent," Guardiola told a news conference on Tuesday. "It's difficult news for him and his family.
"We wish him – everyone at Manchester City from the staff to the chairman, all the people – a safe recovery, doesn't matter the time.
"Health is more important than anything else. I'm sure he's in very good hands, with the best doctors.
"He will take care of himself. I wish him the best recovery as possible and he can come back to play again, otherwise he [can] enjoy his life and enjoy what he has done.
"I don't know what he has, but now he knows it [that there is something wrong], he has to be careful and safe for the rest of his life."
Aguero joined Barcelona in the summer on a free transfer from Manchester City, where he became the club’s all-time top scorer with 260 goals in 390 games during a ten-year spell.
