The Argentine Football Association said on its Twitter account that the Manchester City forward 'had a blackout and was taken (to hospital) so routine examinations were made only as a precaution'.
Kelechi Iheanacho inspired the Nigeria fightback.
Argentina only secured its spot in the next World Cup in the last round of South American qualifiers and has not delivered convincing performances without Messi.
Banega curled in a free kick, awarded after Nigeria goalkeeper Daniel Akpeyi picked the ball up outside his area, in the 28th minute and Aguero finished off a sweeping counter-attack eight minutes later.
Alex Iwobi later doubled his efforts with a cool finish in the 73rd minute doing a nutmeg on Barcelona's Javier Mascherano.
Nigeria come into the game off the back of a 1-1 draw with Algeria in their last World Cup qualifying - a game that they did not need to win, having already booked their place in Russian Federation next summer.
"It's a hard game to explain", said Sampaoli.
"His suggestion will be tabled at the CAF Executive Committee meeting very soon and we hope they approve it so that we can play a friendly match in March. I know we are capable and have the individual talent to be able to get out of these situations and I'm anxious about what happened tonight".