After a further two sessions were lost on the second day, play eventually resumed at 3.45pm. SA had already lost Aiden Markram and David Bedingham in the space of two deliveries late on Sunday, leaving them 20/2 after 12.2 overs.
There was little respite for the hosts, with Marques Ackerman and Matthew Breetzke also departing early to leave the Proteas 47/4 after 23.5 overs.
Boland was the chief destroyer, producing another disciplined spell to claim Markram, Bedingham, Ackerman and Ryan Rickelton, decimating the SA batting stocks.
Mitchell Starc removed Breetzke, while Josh Hazlewood was almost unplayable at the other end.
Bavuma once again found himself carrying much of the responsibility with the bat, having negotiated the Australian attack with considerably more authority than most of his teammates.
But the scorecard only tells part of the extraordinary story of this Test, which has been dominated by the weather and the condition of the St George’s Park outfield.
Australia won the toss on Sunday and opted to field, but the contest barely had time to settle before rain intervened.
The hosts managed only 12.2 overs on the opening day, with Markram and Bedingham falling to Boland in consecutive deliveries to leave the hosts 20/2.