Ngcobo was substituted off just over 70 minutes into his full PSL debut on Friday evening as Chiefs played to a 1-1 draw with SuperSport United at the Mbombela Stadium.
The Amajita star looked in some discomfort as he was forced off on a stretcher, and was subsequently replaced by Philani Zulu.
The club have since confirmed an Achilles injury for the 19-year-old, who recently helped the national under-20 side qualify for the FIFA U-20 World Cup in Poland.
The former Amakhosi reserve team captain is set to undergo further tests on Monday to determine the exact extent of his setback.
Chiefs remain without Itumeleng Khune, Lebogang Manyama, Happy Mashiane, Jospeh Molangoane, Erick Mathoho and Lorenzo Gordinho due to an assortment of injuries.