Uganda top Group D with 10 minutes, as it stands.
William Luwagga Kizito's cool 10th-minute and only goal of the opening half has ensured that the Uganda Cranes go into the break ahead of Bostwana in Francistown.
This Africa Cup of Nations Group D qualifier is being played at Francistown Stadium.
Midfielder Tonny Mawejje showed great vision as he dipped a long-range cross forward, the lobbed pass finding Kizito who controlled the ball neatly, beat the keeper and finished coolly to give the visitors an early lead.
The two sides are meeting for the fifth time, with Uganda having won two of the previous four meetings. The other two fixtures ended goalless.
As it stands, Uganda tops Group D with 10 points ahead of second-placed Burkina Faso who play on Sunday against Comoros.
Botswana are currently on six points while Comoros lie rock-bottom with three points.