Marnus Labuschagne's spot for the third Test appears in doubt, with Australia's main training session in Cape Town hinting at a top-order shake up.

Labuschagne did not bat in the first rotation in the nets at Newlands on Sunday as he normally does, instead bowling leg spin before a lengthy chat with coach Andrew McDonald and Steve Smith.

It came as Cameron Green, Josh Inglis and Beau Webster initially faced Mitchell Starc, Pat Cummins and Nathan Lyon in a centre-wicket net session.

Labuschagne then spent time facing Josh Hazlewood Scott Boland, Webster and Matt Kuhnemann later in the session.

Interestingly, Smith only faced throwdowns in the nets out the back out of the ground for around 15 minutes, after battling neck soreness in the second Test loss last week.

Australia's selection for the third and deciding Test against South Africa is one of the most intriguing in years, after the thrashing in Gqeberha.

Nic Maddinson is expected to be dropped, with Matt Renshaw an option to go to the top of the order after facing the new ball at an optional session on Saturday.

Green will almost certainly return as a batter only, with the fact he has faced the quicks for so long on Sunday a potential sign he could come in at No.3.

Inglis is available again after recovering from a fractured finger, while Cooper Connolly and Sam Harper also remain on the tour as options.

Webster and Labuschagne finished the last Test as the other two players aside from Maddinson under the most pressure, after also misfiring over the past few months.

Labuschagne has been dismissed for between 30 and 49 in six of his past nine innings, with Cummins noting last week those scores did not win many matches.

The Queenslander's last century came 48 innings ago in the 2023 Ashes, with his average in his past 37 Tests half of what it was in his first 30.

"His 30s have been frustrating for him in the way that he's been playing so well to that point," wicketkeeper Alex Carey said.

"That is the game of cricket. You can't give an inch any time, and he's really hungry, and understanding that his role is to go on and convert those runs. 

"So, again, keep doing what he's doing, but do it for longer. That is what he's thinking as well."

Australia must also decide what to do with their bowlers on a Cape Town wicket that appears drier and with limited grass coverage.

If Lyon is brought back after being left out for Gqeberha, selectors will likely have to leave out one of Hazlewood, Starc or Boland.

Boland claimed his third five-wicket haul in the second Test, but has only once been picked ahead of Hazlewood, Starc or Cummins when all are fit since his debut in 2021.

Australia have not dropped more than two players for a match mid series since George Bailey became chief selector and Cummins captain ahead of the 2021-22 Ashes.