Lieutenant General Lawrence Mbatha is heading a delegation that discussed "issues relating to military cooperation and interaction" with their Russian counterparts, the agencies said, citing the Russian defense ministry.
On Monday, Mbatha "visited educational institution of the ground forces and enterprises of the military-industrial complex" of Russia, agencies said.
"Agreements were reached to further increase cooperation between ground forces in various fields," Russian agency Interfax said.
South Africa has refused to condemn the conflict in Ukraine, which has largely isolated Moscow on the international stage.
The country - an African powerhouse that also wields moral clout for its victory over apartheid - says it wants to stay neutral.
But critics cite a number of recent incidents as evidence of a tilt towards the Kremlin.
On Friday, following the scandal, Russian President Vladimir Putin spoke on the phone with Ramaphosa.
Both leaders agreed to "intensify mutually beneficial ties" according to the Kremlin.
Last Thursday the U.S. ambassador to Pretoria Reuben Brigety said that the United States believed weapons and ammunition had been laden onto a Russian freighter that docked at a Cape Town naval base in December.
South African President Cyril Ramaphosa said the matter was "being looked into" and "in time we will be able to speak about it."
The U.S. welcomed the promises to probe the allegations.
