Aguero lasted just 20 minutes before being replaced by Carlos Tevez and is now set to undergo tests to determine the extent of his injury.
"He had been having a great time and was playing well," said Nicolas Otamendi after the match, who also revealed that Aguero had been crying in the dressing room following his injury.
Gerardo Martino, meanwhile, refused to speculate on the severity of Aguero's latest setback but insists the injury is not linked with the one he was carrying before the international break.
"He had been carrying a knock with his club, during the week we took good care of him," said the Argentina manager.
"He was moving around the pitch well, but unfortunately he felt some discomfort and we are going to lose him.
"I haven't spoken to the doctor but I can confirm the injury is not the same as the one he had been carrying with his club."
The City striker is the latest name on Argentina's growing casualty list. Lionel Messi, Ever Banega, Enzo Perez and Marcos Rojo had already withdrawn before Thursday's defeat.