Aguero, who ended a 10-year spell with City at the end of last season, had to be substituted during Barcelona's 1-1 LaLiga draw with Deportivo Alaves after feeling dizzy and suffering apparent discomfort in his chest.
The City great was sent to hospital for a cardiac exam and will now not be available for Barca until at least February, with treatment in that time set to determine the extent of his recovery process.
The news came as a shock for Barca given Aguero had started just two games for the club since joining from City, and the Argentinian has been in Guardiola's thoughts.
"I sent a message to him through his agent," Guardiola said. "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."
Kyle Walker joined Guardiola for media duties ahead of a Champions League game against Club Brugge and was also rocked by the situation affecting Aguero, a team-mate of his for four years.
Walker also played at Tottenham alongside Christian Eriksen, who is yet to return to the pitch since suffering a cardiac arrest during Denmark's first Euro 2020 match, and such scares seemed to put life into perspective for the England international.
"It's a shock when it happens to anyone," Walker said. "I played with Christian [Eriksen]. You think about them and the family. I'm glad they're okay.
"We're all fit athletes and train hard every day. You have to take precautions and his health is more important than football at the minute.
"We're all human in more ways than one. We make mistakes, we put in good performances. Health is key, without health you're nothing.
"As long as Sergio's okay… I know Christian is because I spoke to him a couple of weeks ago. I spoke to him on text, said I hope he's okay.
"I played in the game at Spurs when [Fabrice] Muamba went down. Seeing it happen with a few people which isn't nice.
"The main priority is health, [Aguero] should take as much time, being fit and healthy is the main priority."