The Russian consulate in Cape Town tweeted a photo of the ship, the "Admiral Gorshkov", in the harbour, saying it was on "its way to Durban where it will take part in joint... drills".
The exercises dubbed "Mosi", which means "smoke" in the local Tswana language, are scheduled for February 17 to 27 off the port cities of Durban and Richards Bay.
They will coincide with the first anniversary of Russia's invasion of Ukraine on 24 February.
More than 350 South African armed forces will take part in the exercises "with an aim of sharing operational skills and knowledge" with Russia and China, the South Africa military said last month, the second such exercises between the three naval forces.
The Zircon missile system on the Russian frigate "has no equivalent", President Vladimir Putin was quoted as saying last month at the launch of the warship for a training mission in the Atlantic and Indian Oceans and the Mediterranean Sea.
"I am sure that such powerful weapons will make it possible to reliably protect Russia from potential external threats," Putin was quoted by Russian news agencies as saying.
South Africa has refused to condemn the invasion of Ukraine which has largely isolated Moscow on the international scene, saying it wants to stay neutral.
South Africa's largest opposition group, the Democratic Alliance (DA), has denounced the joint drills.
"This vessel will be sailing towards the Black Sea and taking part in the invasion against Ukraine," said Kobus Marais, a DA member of parliament with oversight of party's stance on defence, told AFP.
"That can very easily make South Africa complicit in these war crimes," he said. "We are drawn into the propaganda show of Russia."
The Russian consulate and embassy in South Africa did not respond to an AFP request for comment.
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