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The Bafana Bafana international will play in South Africa's top-flight for the first time this season, following a successful stay at Genk.
The defender, who was contracted to the Belgium Pro League club for nine years, spent last season on-loan at French side Troyes.
Ngcongca will add valuable experience to the Sundowns ranks and will fill the void left by former captain Ramahlwe Mphahlele.
Ngcongca can play either at right-back or centre-back.