Thapelo Maseko scored the decisive goal in the second half at the Mexico City Stadium, securing all three points for Bafana Bafana and a place in the Round of 32.
The victory saw South Africa finish second in Group A with four points. They had earlier lost 2-0 to Mexico in their opening match before playing a 1-1 draw against Czechia.
South Africa joined Egypt, Algeria, Ivory Coast, Ghana and Morocco as African teams that have recorded at least one win at the tournament.
Ivory Coast became the first African side to win a match at the World Cup after defeating Ecuador 1-0 in their opening fixture, while Ghana followed with a 1-0 victory over Panama.
Morocco recorded Africa’s third win after beating Scotland 1-0 in their second Group C game before defeating Haiti 4-2 in their final group match.
Egypt secured a 3-1 victory over New Zealand, while Algeria defeated Jordan 2-1 to become the fifth African nation to claim a win.
Meanwhile, Senegal, Cape Verde, DR Congo and Tunisia are still searching for their first victories at the tournament.
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