The news was confirmed by Bafana Bafana twitter account on Sunday morning that the 49-year-old had passed away.
According to reports in the local media, Phil Masinga had been admitted to hospital early last month with an illness.
Sad day for South African football. A loyal servant of the game, on and off the field of play, SAFA President Dr Danny Jordaan was quoted as saying by the same twitter account.
Masinga made 58 appearances for the South African national side, where he also lifted the 1996 Africa Cup of Nations title.
The former Leeds United striker also scored the famous goal against the Republic of the Congo to send Bafana to the 1998 World Cup.