Goals from Robert Wurube and James Moga helped South Sudan complete a 4-1 overall victory in the Central Eastern Zone qualifier to set up a meeting with Uganda in the next round.
On Saturday, Malawi and Seychelles went out to Madagascar and Mauritius respectively.
The CHAN - a tournament for locally-based African players featuring in their own country's domestic leagues - will be staged in Kenya from 12 January to 4 February 2018.
Malawi were beaten 1-0 at home in the second leg of their opening Southern Zone qualifier with Madagascar winning 2-0 on aggregate.
Seychelles could only draw the second leg of their qualifier in Mahé 1-1 as Mauritius progressed 3-2 overall.
Madgascar had Rokotoarimaldla Tsilavina to thank for their victory in Lilongwe as he scored the only goal just after the break, beating advancing Malawi goal-keeper Ernest Kakhobwe.
The visitors were then the better side for most of the second half, displaying offensive and passing football.
Malawi were left to rue their three missed chances in the first half with striker Muhammad Sulumba the main culprit after his weak shot from inside the six-yard box was easily stopped by the Madagascar keeper.
The defeat to Madagascar means Malawi's new coach Ronny Van Geneugden is without a win in three games.
The result will provide food for thought for Malawi who bolstered their squad on return from Madagascar by including among others former captain Joseph Kamwendo and forwards Binwell Katinji and Ishmael Thindwa .
Madagascar will play Mozambique in the next round.
On a good day for Indian Ocean nations, Mauritius sealed their place in the next round of the CHAN qualifiers with a 1-1 draw against Seychelles at the Stad Linité in Mahé to progress 3-2 on aggregate.
On a rainy afternoon, Mauritius opened the scoring with a 14th minute goal from defender Marco Dorza.
Mauritius thought they had doubled the lead but Kevin Perticot's goal was disallowed for offside.
Seychelles then scored two minutes after the break from a penalty having also had a goal disallowed, but they could not add to their tally, with Mauritius booking their place against Angola in the next round.
South Sudan booked their place in the next round of regional qualifying for the 2018 African Nations Championship (CHAN) on Sunday, defeating Somalia 2-0 in Juba.