Amajita advance to the U-20 Africa Cup of Nations final after defeating Nigeria 1-0 in the semi-finals on Thursday evening.
South Africa coach Raymond Mdaka made a few changes from the win over Democratic Republic of Congo, as Kutlwano Letlhaku, Kgomotso Madiba, and top scorer Thabang Mahlangu were brought into the starting line-up.
The Flying Eagles came into the clash on a high after eliminating defending champions Senegal on penalties three days ago.
The Nigerians enjoyed more of the possession in the early stages of the first half, but they found it tough to carve out clear-cut chances at Fletcher Smythe-Lowe's goal.
Amajita had to wait until the 33rd minute for a chance in the 18-yard area, as Letlhaku's cross picked out Mahlangu in the box but the Nigerian goalkeeper rushed off his line to make a vital interception.
Mdaka responded with a double change after the break, as Shakeel April and Jody Ah Shene replaced Letlhaku and Madiba as the South Africans looked to make more of an impact going forward.
South Africa took the lead on the hour mark on 66 minutes when defender Tylon Smith rose highest to head home Neo Rapoo's cross at the far post.
The Flying Eagles threw everything forward in search of the equaliser for the remainder of the second half, with Israel Ayuma going closest on 88 minutes when his header forced a fine save out of Smythe-Lowe.
The South Africans were able to see out the closing stages of the second half to claim the 1-0 win and book their spot in Sunday's final.
