Cyril Ramaphosa was appointed by Zuma in mid-February following the latter's visit here for the Commonwealth Heads of Government Meeting (CHOGM) summit November last year.
His tour of former LLTE stronghold of Jaffna will be preceded by talks with leaders of the Tamil National Alliance (TNA), officials said.
Kick-starting his two-day visit yesterday, he met President Mahinda Rajapaksa, Opposition leader Ranil Wickremesinghe and the External Affairs Minister G L Peiris.
The South African initiative on the resolution of the Tamil issue dates back to August 2012 when Ibrahim Ibrahim then deputy minister of international relations visited Sri Lanka.
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The South African government has emphasised that lasting peace could be achieved when the reconciliation process is underscored by an inclusive dialogue that addressed rights and freedoms of the Tamils.
However, his effort came under increasing attack from Rajapaksa's nationalist allies, claiming foreign interventions will have disastrous consequences.
"We have seen many dubious international interventions. We stay opposed to international mediation," Nishantha Sri Warnasinghe, the nationalist JHU propagandist said.
"We are concerned about his agenda in Sri Lanka," National Freedom Front spokesman Mohamed Muzzamil said.
His efforts would make South Africa the third country in the history the Sri Lankan conflict to mediate besides India and Norway.
Sri Lankan officials and Tamil leaders had previously visited South Africa to study the country's post-apartheid truth and reconciliation commission.