Stubbs was the only player dropped from the squad that lost by 241-runs at Kingsmead Stadium last week, where he scored 32 and 1 in his respective innings.
Breetzke, who last featured for the senior side in July 2025 against Zimbabwe returns to the Test match arena with a batting average of 37.03 from his two caps.
"Matt has been part of the squad before," said head coach Shukri Conrad.
"The fact that his ODI form is as hot as it is giving him an inside lane and more importantly, it's the attitude and the character Matt brings and has."
Conrad also hinted at changes to his playing personnel ahead of the opening day of the second Test in Gqeberha, while confirming that Ryan Rickelton will be taking over as wicketkeeper for the match.
"With Ricks taking the gloves, there are decisions to be made over whether he does move down the order or whether he can continue to open the batting, which he has done before, added the coach.
"There's a few things to consider before we look at the final XI, but we are hell of excited. But we have had the opportunity to lick our wounds and turn this ship in the right direction."
The home side are set to welcome back star seamer Kagiso Rabada, who sat out of the previous match due to a hamstring issue.
South Africa Second Test squad
Temba Bavuma (c), Aiden Markram, Wiaan Mulder, Senuran Muthusamy, Anrich Nortje, Dane Paterson, Kagiso Rabada, Ryan Rickelton (wk), Kyle Verreynne, Marques Ackerman, David Bedingham, Matthew Breetzke, Corbin Bosch, Gerald Coetzee, Simon Harmer, Marco Jansen, Keshav Maharaj.
Australia seamer Mahli Beardman took an excellent 6/24 on his One-Day International debut as they beat England by seven wickets in Perth on Friday to take a 1-0 series lead.
Australia captain Pat Cummins has dismissed Usman Khawaja's claims that the entire team knew about the use of sandpaper on the ball in the series in South Africa in 2018 as "complete and utter nonsense".
The Springboks will look to secure their position at the top of the southern section of the Nations Championship at Stade de France against a French team still seeking revenge for the 2023 Rugby World Cup quarter-final.
The World Test Championship (WTC) is unlikely to expand beyond its existing nine-team format, despite growing calls to include all 12 Full Members in the next cycle.
