Aguero, who is leaving the club at the end of the season, has been troubled by a muscular problem.
Asked if the Argentinian would be available for the Wembley tie, Guardiola said at a press conference: “No, not yet.”
Guardiola has no fresh injury concerns following his side’s memorable Champions League quarter-final win over Borussia Dortmund in midweek.
Guardiola said: “They are OK. Tired, but OK.”
Phil Foden was outstanding in Wednesday’s victory over Dortmund having been selected ahead of Raheem Sterling.
Guardiola insists it does not have to be one or the other, however, as he feels both could thrive in the same team.
He said: “Of course they can play together, they have played many times together. Phil can play in five positions and ‘Rash’ can play in three positions. Everyone can play in a few positions. It depends on them.”