Star batsman de Villiers was ruled out of the series with a left elbow injury that required surgery with du Plessis seamlessly taking over.
His vision has been praised in steering the team to an unassailable 2-0 lead. A win in the final day-night Test in Adelaide next week will consign Australia to their first home series whitewash in history.
Despite this, selectors are not considering promoting du Plessis to do the job full-time.
"AB is still the captain."
Officials hope de Villiers will be fit for the home series against Sri Lanka, starting on December 26.
"We will be guided (as to when he can play) by the medical team in terms of where he is and in terms of match fitness," Zondi said.
"He has been away for five months -- a long time. For starters, he has to be match fit."
It was a fifth straight defeat for Australia which saw chairman of selectors Rod Marsh quit, with Trevor Hohns temporarily replacing him.
The third and final Test starts on November 24 in Adelaide.
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