Amajita finished top of Group B after picking up seven points from three games.
The South Africans had a good response having being held to a 1-1 draw by Madagascar, who also qualified for the semifinals, in their previous game.
It only took 20 minutes for coach Helman Mkhalele’s charges to get a lead in the game as Sinejongo Mkiva started the goal festival.
Striker Rahim Milazi didn’t take long to join the party when he got Amajita’s second goal of the match two minutes later.
The game looked to be all taken away from Lesotho before the half-hour mark, but they didn’t just sit back as they tried to get back into the game.
But, it was South Africa who would get another goal, this time around coming through skipper Rowen Human in the 41st minute to make it 3-0 for Amajita going into half-time.
With Amajita well in the driving seat, Lesotho did manage to have some goalscoring chances but could not take them.
Things got worse for Lesotho when Keletso Sifama finally got to register a goal, after his earlier effort hit the crossbar, to make it 4-0 for Amajita in the 51st minute.
Having not had many saves to make on the day, Amajita goalkeeper Bontle Molefe was handed a real test in the last three minutes of the match, but he ended up making good save.
Amajita will now face Madagascar on Thursday for the second time in the competition with a spot in the final at stake.