The Manchester City striker became Argentina's third-highest scorer in history when he netted in the first half to put the Albiceleste 2-0 ahead.
At the break, however, Aguero suffered an as yet unknown problem and was forced to leave the Stadion FK in Krasnodar and seek medical treatment.
[PARTE MÉDICO AGÜERO] Tuvo un cuadro de lipotimia motivo por el cual fue trasladado a realizarse estudios de rutina sólo por precaución.— Selección Argentina (@Argentina) 14 de noviembre de 2017
TyC Sports later reported that the forward later recovered consciousness and underwent tests in hospital, while Dario Benedetto replaced him on the field.
Argentina later clarified that their striker had been treated as a precaution, and that routine tests were carried out.
"Aguero suffered a collapse and was therefore taken to carry out routine studies merely as a precaution," the federation explained via Twitter.
Without Aguero, Argentina fell to a 4-2 defeat, with three of Nigeria's goals coming after half time.