Covers were brought onto St George's Park around 45 minutes before the 9:45am (6:45pm AEDT) start time, with an attempt to start at 10:25am also aborted.
More rain is forecast further into the morning, with Australia to resume at 4-156 and still trailing South Africa by 170 runs after being asked to follow on.
Wednesday was one of the darkest days for Australia this decade, after they collapsed to be bowled out for 99 in the first innings.
That has put significant pressure on the likes of Nic Maddinson, Beau Webster and Marnus Labuschagne, all of whom have already been dismissed in the second innings.
A total of 98 overs are meant to be bowled on Thursday, but it would have been unlikely all were available even before the rain given the issues with light late in the day.
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 a stiff neck on day four.
Smith has not yet batted in the second innings, as Australia's medical staff bumped 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 he and Josh Inglis would be on the selection table 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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