Play was halted shortly after Jean Kouassi gave the Elephants a 3-1 lead with players from both sides ushering the visibly disoriented match official, Charles Bulu, off the field.
The Ghanaian referee collapsed before making it to the sidelines and had to be stretchered off to receive medical attention.
At international level, the fourth official is usually appointed as the replacement if the referee is unable to continue to officiate the game.
However, the fourth official, Koussi Biro, was ineligible to take charge of the Group K clash on account of being Ivorian.
After deliberating with his colleagues, Kenyan linesman Gilbert Cheruiyot blew the final whistle in 90th minute without playing any additional injury time despite the long delay.
Despite losing the game 3-1, Ethiopia clinched qualification to AFCON 2021 due to Madagascar's failure to beat Niger.