Abraham Ndugwa's goal, a minute into the second half was enough to see off the Sudanese.
Vipers SC have qaulified for the first round of the CAF Champions League on away goals after defeating El-Merriekh 1-0 at St Mary's Stadium Kitende.
Vipers looking to be the second Ugandan side to qualify for the group stages after KCCA, lost 2-1 in Khartoum but needed just a 1-0 to qualify.