Nigeria secured top spot in Group D with a 2-0 victory over Guinea-Bissau on Wednesday night.
With qualification to the next round already secured, Augustine Eguavoen opted to rest Samuel Chukwueze, Moses Simon and Taiwo Awoniyi, as Alex Iwobi, Umar Sadiq and Chidera Ejuke were drafted into the attack.
Guinea-Bissau, meanwhile, were looking for their first win to sneak in the knockout stages after starting with a draw and a loss in the group.
While the sides could not be separated in the opening 45 minutes, Nigeria got the opening goal through Umar in the 56th minute after a fine assist from Kelechi Iheanacho.
The win was sealed with 15 minutes left on the clock, with William Troost-Ekong opening his account for the tournament while Orlando Pirates defender Oliseh Ndah was brought on for the final 15 minutes of the game for Nigeria.
Egypt qualified for the round of 16 after defeating Sudan 1-0 at the Stade Omnisport Ahmadou Ahidjo.
The Pharaohs got their first win in the last game after Mohamed Salah' solitary strike secured a 1-0 victory over Guinea-Bissau.
Egypt had their fate in their own hands and they managed to get the opening goal in the 35th minute, with Mohamed Abdelmoneim nodding home a cross from Abdalla El Said.
In the end, Abdelmoneim's goal proved to be enough for the seven-time winners who finish second in the group and join Nigeria in the knockout stage.
Sudan, meanwhile, finish third with one point from three matches.
