Morocco led Group A with nine points, while Botswana advanced to the quarter finals as one of the top third-place finishers.
Title holders Nigeria will play Cameroon at Stade Mohamed V Stadium in Casablanca on Thursday after the Super Falcons finished second in Group C following their 4-0 win over Burundi on Sunday.
Thursday's other match will see Group C winners South Africa taking on Tunisia at Stade Prince Moulay Al Hassan in Rabat.
Zambia will take on Senegal at the Stade Mohamed V in Casablanca in the first game of Wednesday.