The fourth official, who is reported to be of Ivorian nationality, was unable to take his place and the match was accordingly called off prematurely, with the hosts leading 3-1 at the time of the final whistle.
This was confirmed by the Ethiopian Football Federation, who revealed that a CAF decision was expected to follow in due course.
"The game has been cancelled," the EFF said in a statement. "The referee has been taken to hospital because he fell sick and fell on the field. CAF decision is expected."
While it remains unclear as to how the outcome of the match will be decided, the result is of little consequence for both Ethiopia and Ivory Coast, as Madagascar's failure to beat Niger in the afternoon's other match sees both nations qualify for next year's AFCON.
Ivory Coast 3-1 Ethiopia
Niger 0-0 Madagascar
CAR 0-1 Mauritania