The Bafana Bafana right-back was replaced in the 53rd minute of Genk’s 3-1 victory, which guaranteed top spot in their group and a place in the Last 32.
Reports in Belgium have confirmed that it is a back problem that forced Ngconcga off, and he will be in a race to be fit for Sunday’s League clash with OH Leuven.
It is the second year in a row that Genk have finished top of their Europa League pool, achieved with still one round of matches to play on December 12.
Genk will face Swiss side FC Thun in their final group fixture, who have already been knocked out of the competition after they, and their South African-born defender Lukas Schenkel, lost 2-1 at Rapid Vienna on Thursday. Schenkel was a second half substitute.
Dino Ndlovu’s Maccabi Haifa have also been dumped out of the competition, after losing 2-0 to Dutch outfit AZ Alkmaar.