"CAF has referred the matters to the disciplinary board for investigation and has called for appropriate action to be taken if the identified persons were to be found guilty of any wrongdoing," said African football's governing body in a statement.
Tensions spilt over on the pitch at the end of Saturday's game in Marrakesh, which Nigeria won 2-0 thanks to second-half goals by Victor Osimhen and Akor Adams.
Any disciplinary action could have an impact on the Super Eagles as they prepare for their semi-final showdown on Wednesday against Morocco.
However, CAF said it was also investigating incidents in Friday's last-eight tie between the hosts and Cameroon.
Morocco won that game 2-0 in Rabat, and the Indomitable Lions were notably unhappy at the officiating, in particular the refusal to award them a penalty for a challenge on Manchester United's Bryan Mbeumo in the second half.