City host the newly-crowned Spanish champions on Friday, 7 August holding a 2-1 lead from the last 16 first leg tie back in February.
But Aguero, who has scored 23 goals in 32 games this season, looks set to miss out having failed to recover from the knee injury he suffered in our win over Burnley last month.
Asked if the Argentine will be able to feature against Los Blancos, Guardiola said: “No, i think it will not be possible for the timing.”
City signed off the Premier League season with an impressive 5-0 win over Norwich.
It was a fine end to the campaign, with City registering 100+ goals in the Premier League for the third time.
But Guardiola insists this game will mean nothing when we face Real Madrid and says a high-quality two-week training programme is needed to ensure his players are in peak condition.
“Different competition, different opponent, cannot compare,” he added. “We have two weeks.
"We are going to start to prepare the game, tell them what they should do, try to play the game, do a good game. Arrive in best conditions and we are going to do it.”