Bio Odo Chabi opened the scoring for Benin in the second half before WAFA midfielder Prosper Ahiabu pulled parity to share the spoils.
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The Black Satellites booked their ticket to the tournament on a 4-1 aggregate scoreline - winning the first leg 3-1 in Cape Coast a week ago before making the trip across to Benin for the return encounter.
Ghana join Burkina Faso, Burundi, Mali, Nigeria, Senegal, South Africa and hosts Niger as the teams to qualify for the 8 team tournament.
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The tournament will take place in Niger between 24 February – 10 March 2019.
The top four teams will qualify as CAF’s representatives for the 2019 FIFA U-20 world cup to be hosted in Poland in May.