Smith had loomed as Australia's main centre of resistance in their first-innings horror show, as the tourists slumped to 99 all out in reply to the Proteas' 9-425 declared on Wednesday.
But though he had looked in good touch through the first 55 balls of his innings, Smith required medical treatment after flinging his head around following an edge off Kagiso Rabada.
From that point on, he was a different batter.
While his movements were exaggerated before the treatment, he either mishit or played-and-missed at four balls from Rabada's next over while moving into strange positions.
The right-hander even began getting himself front on to bowlers before some deliveries through the rest of his innings, and twice required medication on field.
And after being bowled by Wiaan Mulder for 28, Australia's vice-captain did not bat at No.4 when the tourists were asked to follow on and went to stumps at 4-156.
Instead he sat with a cushion around his neck limiting its movement, which has been an ongoing issue.
"We felt it was best to hopefully get the batting unit through to tomorrow and then hopefully he's better placed," Australia's coach Andrew McDonald said.
"We've seen the physio working on him, so he'll bat tomorrow.
"It's not something that will rule him out of the innings, but it was just a little bit more time than we expected on the back of the first innings.
"Sometimes he changes his technique when he's fully fit too, but he was limited in what he could do."
Australia's capitulation on Wednesday marked their worst first-innings batting showing since the horrors of Hobart against South Africa almost 10 years ago.
But McDonald remains adamant there is a path to saving the match and keeping a 1-0 series lead headed to the third and final Test at Cape Town.
The tourists trail by 170, and will likely need to wipe out that deficit on Thursday and bat enough time to give some hope of a draw.
There is only a small chance of morning rain after wet weather ruined the first two days of the Test, but light means the allotted 98 overs are unlikely to be bowled.
"I have great belief and trust in the skill sets in that room, and in particular tomorrow, we'll go out there and potentially turn this one around," McDonald said.
"If that doesn't unfold, we'll go to Cape Town and we'll reload. We'll go again.
"A great strength of this group is on significant setbacks - and I'll say this is a significant setback - we've been able to respond."
23°C