The 1986 World Cup winner Argentine said his "neck hurt a lot".
The 57-year-old posted a photo on social media showing medical staff with him at half-time during the game but denied any reports of having been taken to hospital.
"I want to tell everyone that I am fine," read part of his Instagram post.
"I was checked by a doctor and he recommended me to go home before the second half, but I wanted to stay because we were risking it all. How could I leave?"
Argentina's controversial win over Nigeria saw them earn a slot in the last 16 and will now face off with the 1998 World Cup champions of France on Saturday.
Maradona was seen tearing down during the game with the scores at 1-1, a scoreline that would show Argentina the exit but a late strike from Marcos Rojo ensured that his side progress to the knockout stages of the tournament.
Maradona, a former Argentina national team coach celebrated the late winner by flashing his middle finger.