Ahead of the match, South Sudan strengthened their squad with two new players: Tito Okello from Abelashhar FC and Valentino Yuel Kuach from Murooj FC.
The first half was tightly contested, with both teams focusing on defense.
Sudan took the lead in the 76th minute when Mohamed Eisa scored, but South Sudan responded in the 98th minute when substitute Omot David Sebit netted the equalizer, ensuring a 1-1 draw.
The result was important for South Sudan, which is recovering from a 3-0 loss to Sudan in the first leg.
The draw keeps South Sudan in fifth place in Group B, behind DR Congo, Senegal, Sudan, and Togo, but ahead of Mauritania.
Both teams now look ahead to their next matches, with South Sudan facing DR Congo and Sudan playing Senegal.
On Sunday, the South Sudan Football Association (SSFA) criticized the Sudan Football Association for poor coordination, which left the South Sudan team stranded at the airport in Libya for hours.
After arriving from Cairo, the team waited three hours, with their passports seized by Libyan authorities due to Sudan's lack of coordination in facilitating their entry into Libya.
The delay caused immense stress and hardship for the players, leaving them physically exhausted, sick, and mentally affected.
The SSFA has called on FIFA and CAF to hold the Sudan Football Association accountable and improve the coordination of international travel for teams.