Most of the Senegal team walked off the pitch and angry away fans threw objects as they tried to enter the field of play at the Prince Moulay Abdellah Stadium, with Morocco having the chance to win the final with practically the last kick of the match.
Brahim Diaz eventually took the kick in the 24th minute of time added on but his attempted chip was saved by Senegal goalkeeper Edouard Mendy, keeping the score at 0-0 and sending the final to extra-time.
The penalty had been awarded by the Congolese referee following a lengthy VAR check for a challenge on Diaz by Senegal defender El Hadji Malick Diouf.
Diaz led the protests following that incident, vehemently calling for a penalty to be given as the Moroccan bench joined in.
Stewards and police formed a barrier in front of the small section of Senegal supporters gathered at the opposite end of the stadium, and calm was eventually restored when extra-time began.