Marnus Labuschagne and Usman Khawaja grabbed half-centuries as Australia made the best of a rainy day one to be 147 for two at stumps in the third Test against a frustrated South Africa in Sydney on Wednesday.

Opener Khawaja was 54 not out and Steve Smith yet to face a ball when rain halted play midway through the final session at the Sydney Cricket Ground.

The match is a dead rubber after Australia sealed the series with wins in Melbourne and Brisbane, but Pat Cummins's side can book their place in the World Test Championship final with another victory.

Lion-hearted paceman Anrich Nortje took both the wickets, removing opener David Warner for 10 early in the morning and Marnus Labuschagne for 79 with the last ball of the day.

Labuschagne's dismissal broke a 135-run partnership with Khawaja and came as sweet relief for the Proteas, who might earlier have felt the very heavens were against them.

Their captain Deal Elgar lost the toss for the third time in the series, with Cummins winning his fifth in succession to complete a perfect home summer with the coin.

Labuschagne was reprieved on 70 after nicking Marco Jansen to Simon Harmer at first slip, the spinner claiming a low catch that was cancelled out by the third umpire despite replays appearing inconclusive at best.

South Africa were left stewing over the decision when bad light and rain brought an early tea.

Nortje helped set things to rights after a prolonged break with a fast and furious ball that cramped Labuschagne and found the outside edge on the way to wicketkeeper Kyle Verreynne.

The speedster roared in triumph but South Africa's celebrations were cut short by the rain.

Nortje's first wicket fell in his lap as Warner, blood pumping after two early fours, slashed at a fuller delivery that sent a thick edge to towering all-rounder Jansen in the slips.

Between Nortje's wickets, South Africa had little to crow about.

The pitch was largely unresponsive and Elgar's bowling changes ineffective in the main.

Keshav Maharaj and Harmer, who replaced fast bowler Lungi Ngidi to offer a second spinning option, found some turn before lunch but were smashed out of the attack after the break as Labuschagne hit out.

Kagiso Rabada's underwhelming series continued, the pace spearhead conceding 45 runs from his 12 overs.

Both teams sprung selection surprises, with Australia picking Matt Renshaw to replace injured all-rounder Cameron Green at number six, while dropping paceman Scott Boland in favour of fit-again Josh Hazlewood.

Renshaw, back in the side for the first time in nearly five years, tested positive for COVID-19 before play but was isolated from the team and will play out the Test.

Left-arm spinner Ashton Agar was picked for his first Test since 2017.

South Africa went with wicketkeeper-batsman Heinrich Klaasen to replace Theunis de Bruyn at number three, overlooking Rassie van der Dussen.