An estimated 40,000 spectators took over the 16,000-capacity Ahmadu Bello Stadium in Kaduna as the Super Eagles drew 1-1 with Egypt. However the game ended without any major incidents.
The fine also comes with a stern warning to the federation as regards crowd control with stiffer sanctions to be meted out if such an incident occurred again.
The decision was one of many actions taken during its disciplinary board meeting held on April 18, CAF said.
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Similarly, the Egyptian federation was equally fined $5000 for excessive use of laser beams during the return leg of the Afcon 2017 qualifying game with Nigeria in Alexandria.
The committee also issued a warning about the “security measures in Caf matches” and that in the case of similar incidents, the team may have to play on neutral territory.
Nigeria were held to a 1-1 draw in Kaduna and then lost 1-0 to Egypt in Alexandria, which effectively ended the Super Eagles’ quest to qualify for the tournament in Gabon next year.