Bafana Bafana (The Boys) were hanging on to a lead Percy Tau gave them after 15 minutes when the Lille striker came off the bench.
The 22-year-old also scored on his international debut last Wednesday at the same ground as South Africa scraped past Angola on penalties to reach the final.
He flew to southern Africa this week having scored for French Ligue 1 strugglers Lille last weekend in a 2-1 defeat at second-place Monaco.
Angola edged Zimbabwe 4-2 on penalties after a 2-2 draw to come third as teams took advantage of a FIFA international window ahead of 2019 Africa Cup of Nations qualifiers this year.
Greece-based Djalma Campos starred for Angola as he equalised twice to cancel goals from Abbas Amidu and Talent Chawapiwa in a curtain-raiser to the final.
Tottenham Hotspur midfielder Vincent Wanyama scored twice as Kenya drew 2-2 with the Comoros in Moroccan city Marrakech.
The Kenyan converted an early penalty before goals in each half from Mohamed M'Changama and Djamel Bakar put the Comorans ahead.
Wanyama levelled six minutes from time to spare the 'Harambee Stars' the embarrassment of losing to a nation 27 places lower on the FIFA world rankings.
Ill-prepared minnows Sao Tome e Principe suffered a 3-1 defeat away to Uganda having arrived in Kampala just 12 hours before the kick-off.
Joseph Ochaya, Murushid Jjuko and Abraham Ndugwa gave the home team a commanding lead and Varela Jose claimed a late consolation goal.
Sao Tome are ranked 179 of 211 FIFA nations, but boast one of the most interesting national team nicknames -- the falcons and true parrots team.
Botswana left it late to defeat Lesotho 1-0 in Gaborone with Tebogo Sembowa netting six minutes from time.