The 24-year-old has been sidelined since suffering a knee injury in the Premier League champions’ opening game of the season against Southampton.
However, that blow, which has kept the striker out of action for a month, did not prevent him being called upon by coach Alejandro Sabella for the World Cup qualifiers against Paraguay and Peru.
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"He went there for five days, he worked with the physio. The Argentina manager wanted him there.
"This is a stupid rule because if we had a player who is injured for two weeks it is better he stays here."
Aguero, who finished as the club’s top scorer last term, could make a return to first-team action against Stoke if he passes a late fitness test or may be saved for the Champions League showdown with Real Madrid.
"Sergio is not 100% but his knee is okay. Maybe he could be on the bench,” Mancini added.