Aiden Markram is unbeaten on 111, after the home side won the toss.
The match is the last in what has been a tempestuous series, with South Africa leading 2-1 following their emphatic, and now infamous, 322-run victory in Cape Town, a game that will forever be remembered for an audacious attempted cheat by their opponents.
Former Test batsman Adam Voges then spoke to the group and handed over a new baggy green cap to fast bowler Chadd Sayers, which was followed by a round of hugs.
Sayers and Handscomb were two of four changes in the Australian team.
South Africa vs Australia 4th Test will be played at Wanderers in Johannesburg.
Australia made four changes from the last test, replacing the banned trio with Joe Burns, Matt Renshaw and Handscombe.
Cummins checked South Africa's momentum in the same over, though, finally taking the crucial wicket of Markram - who dabbed one to gully - before swinging one in to have Faf du Plessis (0) trapped lbw from the next ball.
Shortly after, Kagiso Rabada (0) chipped Sayers to mid-off to give Australia more reason to celebrate, although the Proteas bowlers will be encouraged by the opportunities the pitch offered on day one.
Two of Australia's new players were also involved in earlier dismissals.
"The money is twelve times heavier for South Africa as it is for Australia". This will be the fourth Test of the four-match series between the two teams.
The chants over the absence of Smith and Warner were occasional and in pockets, but were a reminder that Australia might have to face up to the embarrassing ball-tampering episode for some time to come.
There were smiles as wicketkeeper Tim Paine was congratulated on becoming Australia's 46th official Test captain.
The Australians had been holed up in their team hotels in Cape Town and Johannesburg since Monday as an internal investigation was carried out into the actions of Smith, Warner and Bancroft.
He'd said a day before that it would be hard, but his team would "be doing everything they possibly can to play and make people proud of them".