Steve Smith has been ruled out of Australia's third Test decider against South Africa in Cape Town after it was confirmed late on Tuesday morning that the batter had not fully recovered from a neck injury.

Australia gave the 37-year-old a chance to prove his fitness ahead of the Test match, which would have seen Smith return to Cape Town for the first time since the infamous 'Sandpapergate' scandal at Newlands in 2018.

Smith appeared to injure himself during his first spell at the crease during Australia's second Test defeat to South Africa in Gqeberha, in which the hosts levelled the series 1-1.

The former skipper subsequently dropped down the batting order in the second innings, as Pat Cummins' side went on to suffer an innings and 31-run defeat.

Ahead of the third Test, Smith had complained of neck stiffness during Australia's pre-match training session and was due to undergo a fitness test ahead of Tuesday's match.

He was later seen walking around Newlands with a large plaster stuck to his neck.

Cummins said that their star batter had been working to overcome the injury early on Tuesday morning, but confirmed at the toss that Smith would be one of four changes to the Australia XI.

"He had a little try this morning," Cummins told SuperSport. "But he wasn't happy with how his neck was feeling, so we had to look elsewhere."

Smith, who received 12-month suspension for his role as Australia's captain in the ball-tampering scandal, has had a lean tour of South Africa.

His top score of 28 came during Australia's first innings in Gqeberha, with Smith having made 25 and 27 during the opening Test in Durban.

Cameron Green returns to the side and slots in at No 4 in place of Smith. Josh Inglis, Cooper Connolly and Nathan Lyon also come into the starting XI.

Beau Webster, Scott Boland and Nic Maddinson miss out, while Matt Renshaw opens for Australia in Maddinson's place.

Australia won the toss and elected to field first, with Cummins stating he was hopeful his batters can bounce back after South Africa's bowlers kept them to a first-innings score of 99 in the second Test.

"We've got some guys really well placed," Cummins said. "They've been here working hard the last couple of weeks.

"A couple of injuries they're coming back from and are now 100 per cent. It's exciting, it's a huge opportunity and everyone's itching to get out there."