Tunisia snatched a stoppage time goal from Ali El Abdi's diving header to edge Madagascar 3-2 in neutral Pretoria and make sure they will finish in the top two in Group A.
That extended to 18 their record run of successive appearances at the finals, to be hosted in Morocco next year.
A 1-0 win for Libya away in Rwanda meant Nigeria were guaranteed a top-two finish in Group D one hour before they kicked off their own match against Benin in Abidjan, but the Super Eagles were then held to a 1-1 draw.
Defender Mohamed Tijani's 16th-minute goal put Benin on course to qualify but they will now have to wait after a late equaliser from Victor Osimhen spared Nigeria's blushes.
Gabon qualified from Group B when their closest challengers, the Central African Republic, went down 1-0 to Lesotho. The result confirmed a top-two finish for Gabon with two games still to play.
South Africa and Uganda also advanced without kicking a ball and are assured a top-two spot in Group K after Congo lost 3-2 in South Sudan.
It was the first points of the campaign for Africa's newest country, who scored a late winner in Juba from Data Elly.
Also on Thursday, Ghana's slim hopes of extending their run of 10 successive finals appearances were handed a lifeline when Sudan were subjected to a 4-0 drubbing by Niger.
Sudan needed only a draw to eliminate Ghana from the running in Group F but suffered stage fright in Lome and were 3-0 down by half-time, two of the goals coming from Ghana-born Daniel Sosah.
Ghana, however, must still win their last two fixtures, away in Angola on Friday and at home to Niger on Monday. Even then, if Sudan take a point from their last game against already-qualified Angola on Monday, Ghana will be out.
Algeria dropped their first points of the campaign as they were held to a goalless drew away by Equatorial Guinea in stifling heat in Malabo. Both teams were already sure of their place at the tournament in Morocco, which will be held from December 21, 2025 to January 18, 2026.
Two sides advance to the finals from each of the 12 qualifying groups with Algeria, Angola, Burkina Faso, Cameroon, the Democratic Republic of Congo, Egypt, Equatorial Guinea, the Ivory Coast, Morocco and Senegal having booked their berths before Thursday's matches.
Senegal beat Burkina Faso 1-0 away in their top-of-the-table clash in Group L.
On Friday, the qualifiers continue with 10 matches around the continent. Home success will see Botswana, Zambia and Zimbabwe join the list of finalists.
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