Masinga was most famous for his long-range strike against Congo at FNB Stadium in 1997, which secured South Africa qualification to its very first Fifa World Cup finals in France the following year.
Masinga was hospitalized in December previous year after suffering from an "undisclosed illness", and was reportedly recovering at the Tshepong Hospital but was reportedly later moved to Parktown in Johannesburg.
The Bafana twitter account confirmed on Sunday that Masinga had sadly passed away.
South Africa Football Association have announced the death of former striker Phil Masinga at the age of 49.
Masinga was also a member of the victorious 1996 Africa Cup of Nations squad.
In 328 professional appearances, the striker scored 154 goals. "The thoughts of everyone at Leeds are with his family and friends".
The center-forward played in the Premier League with Leeds United between 1994 and 1996 before moving to Swiss side St. Gallen and Italian clubs Salernitana and Bari.
South African Football Association (Safa) president Danny Jordaan joined the football world in remembering and mourning Masinga.