Goals from Liam Jordan, Sibongakonke Mbatha and Zama Rambuwane helped seal a 5-0 aggregate victory for Amajita, as they cemented their place at the under-20 Africa Cup of Nations in Zambia next year.
Thabo Senong's side did well to consolidate their 2-0 aggregate lead from the first leg a fortnight ago in the first half, before a few tactical changes saw his charges bag three goals in the second half.
Jordan was first to get onto the scoresheet as the Bidvest Wits striker tapped home unmarked at the back-post after a good passage of play from Amajita in the 50th minute.
Lesotho pushed hard to find an equaliser but the South African defence held firm as goalkeeper Mondli Mpoto also pulled off a few good stops to deny the visitors.
Two goals in the final six minutes from the hosts saw Mbatha fire home after a goal-mouth scramble in the 84th minute, before Rambuwane placed the cherry on the cake in the 89th minute.
The SuperSport United attacker broke in behind the defence with a clinical run that left the Lesotho goalkeeper clutching air as he finished off the move by placing the ball into an empty net.
Amajita XI: Mpoto, Mohamme, Malepe (C), Makumela, Frosler, Mtshweni, Mokoena, Kodisang, Mbatha, Makgalwa, Jordan.
Subs: Johnson, Kammies, Saralina, Mbule, Rambuwane, Sithole, Mayo