Zimbabwe edged the Republic of Congo 2-0 in Harare to top Group G while DR Congo beat Liberia 1-0 in Kinshasa to secure second spot.
President Felix Tshisekedi was among thousands of fans who cheered on the national team as they wrapped up a difficult qualifying campaign.
Tanzania beat Uganda in Dar es Salaam 3-0 to qualify as Group L runners up. Uganda had already qualified with a game to spare.
In Cotonou, Benin beat Togo 2-1 to qualify from Group D. North African giants Algeria led the group.
Earlier on Saturday, Burundians partied late into the night as they celebrated their country’s historic qualification to the Africa Cup of Nations.
Burundi drew 1-1 with Gabon in Bujumbura to finish second in Group C and secured a spot in the Nations Cup finals for the first time in their history. Mali topped the group
Cedric Amissi scored in the 76th minute as Burundi, who only needed a draw to qualify, looked to have sealed their place at Egypt 2019.
Burundi joins fellow East Africans Uganda and Kenya at the finals in Cairo.
Gabon’s Arsenal striker Aubameyang had a largely quiet afternoon and they were unable to get the second goal they needed to reach the finals.
Also on Saturday, title holders Cameroon qualified after beating Comoros 3-0 in Yaounde. Guinea Bissau and Namibia also qualified.
The 24 countries that will play at the AFCON finals are: Egypt (hosts), Algeria, Angola, Burundi, Cameroon, Ghana, Guinea, Guinea Bissau, Ivory Coast, Kenya, Madagascar, Mali, Mauritania, Morocco, Namibia, Nigeria, Senegal, Tunisia, Uganda, Zimbabwe, the Democratic Republic of Congo, Tanzania, Benin and South Africa.