Kenya and Tanzania lost African Nations Championship (Chan) qualifying ties on Sunday, but both will still feature in the 2025 tournament during February.
As co-hosts of a unique national teams competition – only footballers playing in their country of birth are eligible – both are guaranteed places at the finals.
Kenya, Tanzania and fellow co-hosts Uganda, who had a bye, were included in the qualifying process so they could gain competitive match practice instead of relying on friendlies.
After building a two-goal first-round, first-leg lead in Juba last weekend, South Sudan came from behind to draw 1-1 with Kenya in the return match and qualify 3-1 on aggregate.
Austin Odhiambo gave Kenya an early lead in Kampala, which Ebon Malish cancelled by scoring two minutes before halftime in Kampala.
The match was staged in the capital of Uganda because Kenya are renovating stadiums in Nairobi for the 1-28 February Chan tournament.
Tanzania edged Sudan 1-0 in Dar es Salaam through a first-half goal from Crispin Mhagama to level the aggregate score at 1-1, but lost 6-5 on penalties.
Eswatini completed a double over Zimbabwe with a 1-0 victory in the South African city of Mbombela through an Andy Magagula goal midway through the second half.
Magagula netted twice in a 3-0 first-leg win last weekend, and is the leading scorer after the first round.
Eswatini triumphed after overcoming the handicap of being unable to play at home due to the lack of an international-standard stadium. They will play Madagascar next month for a place in the finals.
The victories were plotted by Croatia-born former Zimbabwe coach Zdravko Logarusic, and ended a run of 18 matches without a win by Eswatini in the seven previous Chan qualifying competitions.
Despite being confined to home-based footballers, Chan matches carry full-international status and results count toward the Fifa world rankings.