The victory made it three wins out of three for the side in their Group A campaign and they will now meet Angola on Wednesday in the semi-finals.
Coach Thabo Senong rested a number of his key players with top spot in the pool secured before the kick-off, but the home side still had too much in the tank for Botswana, who end their campaign with three defeats.
Amajita’s latest victory follows wins over Lesotho (8-0) and Swaziland (1-0) earlier in the pool, with the three clean-sheets as pleasing to Senong as the goals scored.
Senong is building his squad for the 2017 African Youth Championships that will be staged in Zambia from late February.