Amajita secured their spot in the final after defeating Egypt 1-0 in the final on Thursday afternoon.
Thabo Senong's charges got off to the perfect start when Lyle Foster put the South Africans ahead after five minutes.
Despite taking the early lead, Amajita found clear-cut chances hard to come by and they had to wait until the 27th minute for their next chance when Luvuyo Mkatshana forced the Lesotho goalkeeper into a fine save.
Amajita eventually doubled their lead five minutes before halftime thanks to a strike from Kamohelo Sambo.
Lesotho did manage to pull a goal back in the 59th minute as Mokokoane fired past Amajita goalkeeper Sanele Tshabalala.
Happy Mashiane had a chance to extend Amajita's lead in the 82nd minute but his strike sailed inches wide of the post.
A few minutes later, Mokokoane nearly restored parity but his powerful free-kick sailed over the crossbar.
2-1 was how the score remained at the full-time whistle as Amajita held on to win the COSAFA Championship.
Amajita XI: Tshabalala; Mabiliso; Sambo; Mukumela; Cupido; Zuke; Mbulu; Mkatshana; Mashiane; Ntsabaleng; Foster.
Subs: Kubheka; Leaner; Cross; Modise; Bull; Maswanganyi; Sibiya