Hundreds of employees of the Eastern Cape health department have been issued with final warnings aft.
The repositioning of the 42.2km event will also see the introduction of internationally competitive cash prizes to lure the world's best runners to the premier event.
Central Gauteng Athletics (CGA) and clubs in Soweto agreed to set up the Soweto Marathon Trust, a body which will include former Athletics South Africa (ASA) chief executive Banele Sindani.
Sindani was one of the people who formed the Soweto Marathon - along with former ASA president Leonard Chuene and development officer Boycie Ntlwane.
Other trustees include CGA president James Moloi, former Two Oceans Marathon winner Thulani Sibisi, Steven Khanyile and Sello Khunou, who is the chairman.
"The trust is an independent entity well-positioned to build the race into a big brand such as the New York Marathon, the London Marathon and others," said Khunou.
"We believe that this positive development heralds a new era in the history of the race, which already attracts runners from Namibia, Zimbabwe, Kenya and Ethiopia.
"The Soweto Marathon is a road race with tremendous potential, yet this potential remains untapped. Instead of growing bigger and better, the race is stagnating at best and deteriorating at worst."
Khunou said the next step was obtaining major sponsorship.
"Our immediate goals are to include strategic partners who share our vision for the race and secure offices for the trust."