Goals in either half from David "Cheche' Ochieng and Clifford Miheso, rekindles Kenya's hopes of reaching the last eight of the tournament
Kenya’s goals came courtesy of David Ochieng and Cliffton Miheso in each half of the pulsating encounter.
Kenya - who were donning an unfamiliar kit of yellow jerseys and black shorts - were by far the better of the two teams as the forward trio of Paul Were, Kevin Omondi and Mike Baraza - who had been given a nod by coach James Nandwa for this duel, running rings around the South Sudan defence almost at will.
Mieno and Were had already missed two clear cut chances by the time Tusker defender Ochieng rose highest from a Kevin 'Daddy' Omondi corner-kick to thunder home a powerful header past a hapless Juma Jenario manning the South Sudan goal.
South Sudan fluffed their only chance of the game on a soggy Namboole pitch that had experienced heavy showers hours before kick-off.
Nice link up play between Thomas Jacob and Adnan Nani provided Kugbour Dar with a good shooting opportunity for South Sudan but the attacking midfielder miscued the chance.
Kenya's Were then broke clear on 30 minutes but skewed his effort well over the bar in a one on one chance.
Kenyan custodian Duncan Ochieng' needed treatment just before the break after colliding with Martin Kamis.
Nandwa seemed to spur his side to score more goals against arguably the weakest team in the Group that comprises Uganda and Ethiopia. After the breather the former Kenyan international replaced Anthony Kimani for Edwin Lavatsa and Paul Were for Clifton Miheso.
However, it was Sudan who are ranked 200 out of 207 teams on the latest Fifa rankings, who controlled the proceedings in the first quarter of the second half but failed to make any meaningful impact.
In the 67th minute, it was Mike Baraza's turn to miss an outright chance. The AFC Leopards striker conspired to place a inch perfect slide rule pass over the bar with only Juma Jenairo to beat.
Moments later, Miheso received a pass from Omondi and let fly a vicious effort that found its way to the back of the net for Kenya's second goal.
Kenya then held on to register the morale boasting victory that improves the team's chances of qualifying for the quarter-finals of the tournament. Kenya had succumbed 1-0 to Cranes in the opening match on Saturday.