He was India captain Rohit Sharma's opening partner in the home T20 series against Afghanistan earlier this year but his place looked under threat as he struggled for runs in the IPL
Aguero passed a fitness test ahead of the match in Buenos Aires but limped off after 24 minutes to be replaced by Carlos Tevez.
Coach Gerardo Martino said the injury to his left leg meant he would not make the game in Asuncion.
"Aguero had a problem from his last game with City, where he played well for 65 minutes," Martino told reporters after the match.
"We looked after him this week, he was moving well, very comfortable, but he felt the strain and unfortunately we are going to lose him."