Farouk Miya hited two first half goals to make it two wins from two games against the same country Lesotho, with the first win being 3-0 at Namboole last Saturday.
Miya kicked a strike in the 6th minute just outside the box to open the scoring, and then swept in the winner 10 minutes before half time from a free kick near the edge.
Allan Kateregga nearly broke the deadlock before Miya’s strikes when he whipped-in cross but went wide.
Lesotho came close to scoring in the 17th minute but Matlama FC’s Mabuti Potloane effort went wide.Later, Left back Sello Bokang forced Onyango into a fine save after stretching to his right to deny the goal.
Miya was then booked for overreaction, just like Lesotho captain Mafa Moremoholo moments later for clipping Okwi right outside the box down the left flank.
Desabre brought in Egypt-based Isaac Muleme Kateregga in the 58th minute after the return.
Uganda tops the group L with 10 points with only two games remaining against Cape Verde and Tanzania.