Lesotho kept up their recent winning ways against their much richer neighbour, winning 2-1 in Lobatse.
With the win, Lesotho move to four points from their two group games and have eliminated last year’s runners-up from the tournament.
Amajita still have to play Namibia on Wednesday, but even if they win that game will only garner three points and cannot finish on top of the group standings, thereby missing out the semifinals.
Lesotho have already eliminated South Africa in the African Youth Championship qualifiers and beat them again in early November in a four-nation tournament in Angola.
South Africa’s hopes in Lobatse faded after Doctor Mampuru was sent off after just 30 minutes for a deliberate handball as he illegally kept the ball out of the goal. Lesotho’s Jeremiah Kamela converted the resultant penalty.
On the stroke of half-time the Basotho struck again with a header from Tsebang Lebata to double the score.
A second yellow card for Lesotho’s Tumisang Bereng just after half-time restored the numerical balance and South Africa sought to fight back with Vusimuzi Nameka scoring one minute after coming on as a 57th minute substitute.
But they did not create enough opportunities to level the game and are now out of the tournament.
Namibia must beat South Africa by two clear goals on Wednesday to win the group.