Nigeria will not be competing at the 2017 African Nations Cup after losing 1-0 to Egypt on Tuesday.
Ramadan Sobhy took advantage of a missed clearance to put Egypt atop qualifying Group G at Borg El-Arab Stadium, where a longstanding ban on fans attending games in large numbers in Egypt was temporarily lifted.
Nigeria faced a must-win game after Chad withdrew from their group earlier this week. Under CAF's rules, all of Chad's previous results are thrown out, leaving Nigeria with just two points from three games and one game remaining.
Teams from groups with three teams are also ineligible from advancing as a group runners-up, ending all hope for the Super Eagles.
Morocco became the first team to officially seal their place with a 2-0 win over Cape Verde, their second win in three days over Africa's highest-ranked side.
Cape Verde's Carlos da Graca was sent off in the 55th minute and Youssef El Arabi netted the resulting penalty. El Arabi added a second goal six minutes later to put Morocco through to the finals.
Senegal are a point away from securing their own spot after a 2-1 win in Niger.
A Moussa Konate penalty was followed by a Pape Alioune Ndiaye goal shortly before half-time, and though Niger got a goal back through Victorien Adebayor's penalty, the visitors held on to win.
Senegal now lead qualifying Group K by six points with two games to play, meaning only two defeats -- and the one in Burundi by at least two goals -- could keep them from playing in the finals in Gabon next year.
Burundi stayed alive with a 3-1 win in Namibia despite falling behind to and early opener by Deon Hotto. But a Pierre Kuizera goal followed by a second-half brace from Fiston Razak secured the three points.
Algeria missed a chance to secure Group J after they were held to a 3-3 draw in Ethiopia.
The hosts took the lead three times, but Algeria were able to respond.
Getaneh Kebede had a brace for Ethiopia while Dawit Fikadu added a third. Islam Slimani and Aissa Mandi provided the first two equalisers for Algeria, and Faouzi Ghoulam's 85th-minute penalty secured a point.
Algeria still lead the group by five points over Ethiopia and six over Seychelles, whose own hopes took a major blow with a a 2-1 defeat in Lesotho.
Dine Suzette's opener for Seychelles was immediately cancelled out by Lesotho's Sunny Jane, and Tumelo Khutlang's 74th-minute goal gave the hosts their first points of the campaign.
Ivory Coast remained atop Group I after managing a 1-1 draw in Sudan.
Max-Alain Gradel provided the opener for the visitors on 17 minuets before Muhannad Tahir equalised on the half-hour mark.
Liberia jumped to the top of Group A after routing bottom side Djibouti 5-0, William Jebor completing his hat trick in the final moments after Anthony Laffor and Sam Johnson also scored.
All three contenders had entered the day level on six points, but Liberia took advantage of a goalless draw between hosts Togo and Tunisia to open a two-point lead.
Emmanuel Adebayor returned for Togo but could not make an impact on the scoresheet.
DR Congo retook the lead in Group B with a 2-0 win in Angola thanks to goals by Joel Kimuaki Mpela and Jonathan Bolingi.
Cameroon remained top after both Group M games finished goalless.
Mauritania remained a point back after their draw in Gambia, while South Africa will need two wins in their final two games to have any hopes after a home draw against Cameroon.
Burkina Faso and Uganda stayed level at the top of Group D after their goalless draw.
They both lead Botswana by a point, though Burkina Faso's home win last week gives them the tiebreaker over Uganda.
Rwanda went level on points with Mauritius in second place in Group H after thrashing them 5-0.
After Dominique Nshuti's opener, Ernest Sugira scored twice in two minutes while Fitina Omborenga and Jean-Baptiste Mugiraneza also added goals.
In Group L, Guinea moved into a tie for second place with a 2-1 win in Malawi, who had a first-half lead through Chiukepo Msowoya but let it slip as Mohamed Yattara and Idrissa Sylla scored for the visitors.