Amajita opened the scoring through leading scorer Thabani Mthembu who converted a penalty in the 20th minute.
The visitors led 1-0 at half-time.
They however, came with guns blazing in the second half attacking from all angles and were awarded with another penalty which Mthembu again scored in the 52nd minute.
Percy Tau increased the score to 3-0 in the 70th minute and Amajita captain, Mbongeni Gumede completed the rout following a nicely constructed move by Menzi Masuku to make it 4-0 in the 75th minute.
Amajita head coach Solly Luvhengo said he was happy with the performance.
"The boys played well against a very defensive Botswana. We managed to settle in well into the second half of the game and score three goals. I am satisfied with the goal average and would like to see the team carry this winning habit going forward."
"This is a good start to preparations for the African Youth Championship qualifiers against Nigeria, the ultimate aim is prepare for obstacle that lies ahead and I would like to see us qualify for the AYC finals," said Luvhengo.
The South Africans meet the same opponents on Tuesday at the Mbombela Stadium on Tuesday in which they will play as curtain-raisers for the Bafana/Mozambique encounter. Kick -off will be at 17h30.
Amajita arrived back in the country this afternoon and will drive to Mbombela on Monday.