At 12 for two, the Proteas were in trouble before Bavuma and Ackerman began trying to rebuild.
The rain soon returned, forcing another interruption, with SA reaching 20 for two before the players were again ushered from the field.
With further showers sweeping through Gqeberha, the first day was heading towards frustration with the forecast for Day Two no more promising than it looked on the opening day.
It was an inauspicious start for a South African side that arrived at its home venue needing to respond after being comprehensively outplayed in Durban.
The tourists won the opening Test at Kingsmead by 214 runs after recovering from 124 for six to post 390 in their first innings, with Matt Renshaw making 190.
SA were then dismissed for 284 before the Aussies set an imposing 421-run target for victory, with Josh Hazlewood’s six for 49 completing the job.
The defeat prompted changes to the SA lineup as head coach Shukri Conrad wielded the axe ahead of the second encounter.
Kagiso Rabada returned after missing the Durban Test with a hamstring problem, while Matthew Breetzke came back into the side after his strong ODI series against Australia.
Ackerman was handed his Test debut, while Ryan Rickelton took over the wicketkeeping duties from Kyle Verreynne.
Tristan Stubbs was the notable omission after scores of 32 and one in Durban.
The changes reflected SA’s desire for greater batting depth after Markram’s 75 was their only substantial contribution.
With Rickelton moving down the order to keep, Ackerman was given the opportunity to open alongside Markram.
Australia, meanwhile, made one change, bringing Boland into the XI for Nathan Lyon.
The decision was shaped partly by the weather and the prospect of a pace-heavy attack, and Boland wasted no time justifying his selection with those two early wickets.