Covers were brought onto St George's Park around 45 minutes before the 9.45am (6.45pm AEDT) start time, with two separate attempts to restart aborted.
Lunch was called for 11.20am local time as the rain stopped and ground staff began moving water off the covers, with a scheduled restart time of 12pm.
Clearer weather is forecast for Thursday afternoon, with Australia to resume at 4-156, trailing South Africa by 170 runs after being forced to follow on.
The number of overs will be reduced, with poor light likely to be a factor later in the day.
Wednesday was one of the darkest days for Australia this decade, after they collapsed to 99 all out in the first innings.
That has put significant pressure on players including Nic Maddinson, Beau Webster and Marnus Labuschagne - all of whom have already been dismissed in the second innings.
If Australia can hold on, they will take a 1-0 lead to next week's third and final Test in Cape Town.
There were some positive signs for Australia on Thursday, with Steve Smith back facing throw downs on field before the rain, after struggling with a stiff neck on day four.
Smith has not yet batted in the second innings, with Australia's medical staff bumping him down the order in the hope his neck would improve.
Also notable was the fact Cameron Green faced Michael Neser during a pre-play net session, in the surest sign yet he will be fit to return in Cape Town next week.
Australia's coach Andrew McDonald said on Wednesday that Green and Josh Inglis would be in the fight for selection for the third Test, with the latter back from a fractured finger.
Cooper Connolly and Sam Harper are the other batters on tour.
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