Silva's contract was due to end on June 30 but the midfielder has agreed to a short-term extension to cover the rest of the campaign.
City fans will not get a chance to celebrate the 34-year-old's 10-year stay at the Etihad Stadium but Guardiola says he will be invited back in the future to say goodbye to supporters.
"He will stay until the end of the season and it is unfortunate he is going to finish his last games here without people but he is coming back and hopefully he can have the big farewell with people," Guardiola told a virtual news conference on Tuesday.
"Always the big clubs become a huge, incredible club when they make these kinds of big gestures to these incredible players for what they have done for more than one decade. David is one of them.
"The situation is what it is. No one wants it, not just for David but for everyone. When everything is returning to normal the club will make an agreement with David and do what they have to do."
Silva and his City teammates will restart the Premier League season with a fixture against Arsenal at the Etihad on Wednesday.
"Players that had long injuries, you have to be careful, especially for the recovered situations," said Guardiola.
"The rhythm, and they don't have it for almost one year. The important thing is they don't have pain, they feel good, they don't have problems and that is the very good news."