Putin said he supported South African President Cyril Ramaphosa's proposal to involve African leaders in talks regarding a peace process for Ukraine, according to the Kremlin's readout of the call.
Friday's call between the two leaders came at the request of the South African side, the Kremlin said.
During their talks, Putin also repeated an offer to deliver Russian grain and fertilizers free of charge to African countries.
South Africa has positioned itself as neutral in the conflict, now in its 15th month. On Friday, officials there hit back at U.S. accusations that a sanctioned Russian ship had picked up weapons from a naval base near Cape Town late last year.
The U.S. ambassador to South Africa said on Thursday he was confident that a Russian ship loaded weapons from the Simon's Town naval base in December, suggesting the incident was not in line with Pretoria's professed neutrality.
Ramaphosa said he had opened an inquiry into the allegation.