Mamabolo (36) was cleared of doping charges earlier this week, after an inquiry committee found multiple irregularities in the testing process.
"We will honour the 2012 Comrades Marathon winner, Ludwick Mamabolo, and present him with his trophy," the Comrades Marathon Association (CMA) said in a statement on Friday.
Mamabolo said he hoped the South African Institute for Drug-Free Sport and the CMA would ensure the rules and processes of the testing process would be followed more strictly in future.
He said athletes should also ensure they were made aware of the correct procedures.
"I just want to be able to compete, to enjoy my running and earn a living as a professional runner," Mamabolo said.
"I hope that this has highlighted the problem and that people realise it's a two-way street.
"I hope this [case] will make things better for athletes and that corrections will be made."
With his build-up hampered by the inquiry hearing, Mamabolo hoped he could challenge again for the Comrades title in KwaZulu-Natal next month.
This year's race is an "up" run from Durban to Pietermaritzburg. The last South African to win the "up" run was Jetman Msutu in 1992.
"We have to always respect Comrades for what it is, but I will do the best that I can, and I am looking forward to it," said Mamabolo. – Sapa