The 26-year-old former TS Galaxy shotstopper has seen his game-time at Amakhosi limited, but he did play in the Carling Knockout last 16 defeat to Stellenbosch.
He was, however, injured while turning out for Bafana Bafana in their final World Cup qualifier with Rwanda in October.
Rwandan journalist Tuyishime Anastash confirmed the news with a picture of Ntwari in hospital.
He posted: "Amavubi goalkeeper Ntwari Fiacre underwent shoulder surgery on Tuesday and will be out of action for his club Kaizer Chiefs for two months."
Chiefs are next in action in their first group stage fixture of the CAF Confederation Cup against Egyptian side Al Masry on 23 November.
