Lyle Foster was a handed a start after his brace midweek and he managed to register an effort at goal after seven minutes but his effort was saved.
Thabo Senong's charges looked more lively in the first half, but they lacked the cutting edge to carve out clear-cut chances.
In the 38th minute, Foster could have broken the deadlock but the Orlando Pirates striker failed to direct his header on target.
Amajita eventually took the lead on the stroke of half time courtesy of a fine strike from Mkatshana.
The second stanza did not produce the same tempo as the first with Amajita happy to defend their one-goal advantage.
Foster almost bagged his third goal of the campaign in the 78th minute but his strike crashed against the post.
Mkatshana's first-half strike was to be the only goal of the game as Mozambique failed to bypass the South African defence on the day.
Kubheka; Mabiliso; Sambo; Mukumela (c); Cupido; Zuke; Matlou: Ngcobo; Ntsabaleng; Mkatshana; Foster.
Subs: Tshabalala; Leaner; Bull; Cross; Modise; Sibiya; Maswanganyi; Mashiane; Mbulu.