The Argentina international injured his foot in the Citizens' 2-1 win over Newcastle United at the start of the month.
Aguero has been used in four of City's five matches since then, but he has only lasted around an hour in each of those games before being taken off.
Speaking ahead of his side's trips to Hoffenheim and Liverpool over the next seven days, Guardiola told reporters: "Sergio is struggling a bit with some problems in his foot.
"He is not 100%. He has not recovered from what happened against Newcastle and we spoke about playing 60 minutes and we were lucky he scored at the right moment."
Aguero's goal in the 2-0 win against Brighton & Hove Albion on Saturday made it five in seven league outings this term.