Togo 2 - 0 Cameroun
In Wednesday's final round of matches, Nigeria were held 2-2 by South Africa in Uyo, meaning they finished outside of their group's top two automatic qualification spots with eight points - a total that also put them out of the running to be the best third-placed team.
South Africa had already assured their place at the tournament, which will be played from 17 January to 8 February.
Congo Brazzaville, Ivory Coast, Ghana, Guinea, Mali and DR Congo all claimed their tickets to the continent's showpiece event with their results on Wednesday.
Algeria, Burkina Faso, Cameroon, Cape Verde, Congo Brazzaville, DR Congo, Equatorial Guinea (as hosts), Gabon, Ghana, Guinea, Ivory Coast, Mali, Senegal, South Africa, Tunisia and Zambia.
- Group D
- Ivory Coast 0-0 Cameroon
- DR Congo 3-1 Sierra Leone
- Group B
- Ethiopia 0-0 Malawi
- Mali 2-0 Algeria
- Group E
- Ghana 3-1 Togo
- Guinea 2-0 Uganda
- Group F
- Niger 1-1 Mozambique
- Zambia 1-0 Cape Verde
- Group A
- Nigeria 2-2 South Africa
- Sudan 0-1 Congo
- Group C
- Burkina Faso 1-1 Angola
- Gabon 4-2 Lesotho
- Group G
- Senegal 3-0 Botswana
- Tunisia 2-1 Egypt
But the Super Eagles blew their chance to prevent a troubled campaign from turning disastrous, even though they fought back from two goals down to finish with a draw.
The writing was on the wall for Stephen Keshi's side, who have been plagued by both on and off the pitch problems, when Tokelo Rantie scored a goal either side of half-time to put the visitors firmly in control.
Sone Aluko pulled a goal back on 68 minutes and Nigerian hopes were raised further when South Africa's Renielwe Letsholonyane was sent off.
In added time Aluko levelled the scores but it was too late for the home side and they once more miss out on playing in Equatorial Guinea, as they did when the country co-hosted the tournament in 2012.
Instead, the runners-up spot in the table - and a place in the finals - was secured by Congo, who beat Sudan 1-0.
Igor Nganga struck the only goal of the game after 63 minutes.
Mali made it through to the finals with a 2-0 win over Algeria, who had already won the group and booked their place.
Seydou Keita scored from the penalty spot, picking himself up to take it after he had been fouled by Carl Medjani, to give his side the lead after 29 minutes.
The advantage was doubled early into the second half when Mustapha Yatabare converted.
It was the first defeat of the campaign for Algeria, who made several changes to their starting line-up, and brought to an end the Desert Foxes' prefect record.
In the group's other match, Malawi and Ethiopia drew 0-0 - a result that ended both sides' chances of making it to the final.
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