The Proteas head coaching position will be vacant at the end of the ongoing T20 World Cup after Mark Boucher decided to step down to take up a coaching role with Indian Premier League (IPL) side Mumbai Indians.
Maketa is the current South Africa A team coach and also served as assistant head coach to the Proteas from 2017-2019 under Ottis Gibson.
The Test series in Australia is important for South Africa as they find themselves in second place in the ICC World Test Championship (WTC).
Commenting on Maketa's appointment, Cricket South Africa (CSA) director of cricket Enoch Nkwe said: "We are pleased to name Malibongwe as our interim coach to lead the Proteas in Australia.
"He is a familiar face to the environment and has worked in the same space previously when he served as assistant coach.
"Mali knows most of the players well; they know him too; and with such a short time between now and the tour, we as Cricket South Africa felt we needed someone who could step in immediately and lead us through what is an important series for the Proteas."
The Proteas will start the Test series Down Under on 17 December in Brisbane before moving on to the traditional Boxing Day Test in Melbourne from 26 December.
The series will conclude with a Test in Sydney from 4 January.