He had been training with the C team at the club after returning from a loan spell last season with French club Troyes.
Ngcongca moved to France after a spat with Genk coach Peter Maes, who the South African accused of racism not long after.
Cape Town-born Ngcongca is still contracted to Genk but obviously has little future at the club while Maes is in charge.
But from Monday, Ngcongca, Tornike Okriashvili and Aleksandr Cavric will be integrated into the reserve team training, the club said.
Tornike Okriashvili is a midfielder from Georgia who got little game time for Genk last season and halfway through the season was loaned to a Trukish club. He is also not in the coach’s plans.
Croatia under-21 international Cavric was also loaned out last season by Genk to Aarbus in Denmark and the Belgian club are again looking to offload him from their books.
Ngcongca has had discussions with Mamelodi Sundowns over a possible move to the Premier Soccer League.