Magqwaka broke the deadlock after the half-hour mark to send the South Africans into the lead at half-time, before Ngubo added the second, following a defensive blunder which saw the youngster poke an effort past the last man and into an unoccupied net.
Amajita booked their place in the final in Maseru, with a 4-3 penalty shoot-out victory over Zimbabwe on Thursday, after the game ended in a goalless stalemate at the end of 90 minutes.
The South Africans struggled early on but shortly before the half-time break, Magqwaka was on hand to convert a corner fed toward the area, into the opening goal, to put South Africa ahead in the 34th minute.
After the interval, South Africa came out striking with chances falling to Tebogo Moerane, Siyanda Ngubo and Nhlakanipho Ntuli, but none were able to add to Magqwaka’s first half effort.
But Amajita were not done yet, as South Africa caught the Kenyans on the break, forcing the goalkeeper to come off his line.
Ayanda Ngubo got to the ball first and toed a shot beyond the goalkeeper and the last line of defence, as the ball stuttered and dribbled towards an empty net and South Africa put the game beyond reach in the 69th minute.
Amajita’s victory saw them lift their fifth title in the competition, having previously won the tournament in 2000, 2004, 2006 and 2008.