Ugandan born striker Tito Okello converted a flawless penalty in the 37th minute to hand South Sudan a lifeline in Group B of the AFCON qualification.
The Cranes were on the front foot and in contention to sealing a berth in the finals of the biannual tournament when proceedings turned against their favour.
A red card in the 31st minute to experienced midfielder Khalid Aucho swung the numerical advantage in the hands of South Sudan.
Moments later, Vipers defender Halid Lwaliwa fresh from a heroic performance in Kampala turned villain when he brought down Daniel Chok in the forbidden area.
Tito Okello sent Onyango the wrong way to hand the Sudanese a deserved lead.
Johnathan McKinstry, Uganda’s coach reacted swiftly into substitution by introducing Mike Azira for Kizito Luwagga in a bid to strike a balance in his team.
In the resumption to the second period, Emmanuel Okwi and Elvis Bwomono were also introduced for Abdul Karim Watambala and Disan Galiwango. Nicholas Wadada also paved way for striker Edrisa Lubega but none of them was equal to the South Sudan resilience.
Farouk Miya got close to snatching a point for Uganda but his free kick hit the cross bar and failed to cross the line.
South Sudan substitute Abdallah Saad Musa also recieved matching orders after committing a second bookable offense.
Following Burkina Faso and Malawi’s 0-0 stalemate in Blantyre, Uganda is still on course to qualification but currently occupy the 2nd place on 7 points behind Burkina Faso on 8 points. Malawi are 3rd on 4 points whereas South Sudan sit bottom on 3 points.
Uganda’s next qualification match will not come until March 2021 when the host Burkina Faso in Kampala.