KAMPALA (AGENCIES) – The game in Kampala looked to be heading for a goalless draw until Halid Lwaliwa, who came on as a replacement for the injured Ronald Mukiibi, headed home a Farouk Miya free kick in the 86th minute.
Before that the best chance had fallen to Miya, who plays in Turkey for Konyaspor, as he saw his shot hit the post in the 72nd minute,
The game also saw a Cranes debut for Elvis Bwomono who plays in the third tier of English football for Southend United, the 21-year-old defender was born in Uganda but moved to the United Kingdom as a child.
The result means Uganda have seven points from their opening three Group B games while South Sudan remain pointless.
The two will face each other again on Monday in the Kenyan capital Nairobi, in a game moved from Juba as the stadium there is being renovated.