Smith had arrived at Newlands before the rest of his teammates on Tuesday, in a bid to convince himself he would be right to face South Africa in the series decider.
The 37-year-old appeared to wear a sticky heat pack on the left side of his neck as he walked into the nets to face batting coach Michael Di Venuto, and received a number of balls.
But with approximately 75 minutes to go before the toss, Smith went to take guard and decided he could not get his head right and walked back down the pitch.
Smith being animated or unhappy in the nets is nothing new.Â
On Monday, as he fought to prove his fitness, he batted for 35 minutes, had a rest, and then grew frustrated as he miss-hit a few balls and packed up his kit and left.
But on Tuesday morning a conversation with coach Andrew McDonald and team medical staff ensued, before chief selector George Bailey ran out of the area.
"I didn't know until I came out to warm up that he wasn't playing," Mitchell Starc, who took 6-72 to bowl South Africa out for 329 and save Australia's day, said.
"I sort-of knew something was wrong yesterday. I was trying to get my laundry at the hotel and couldn't get in the (team) room.
"He's obviously been battling that neck since last week (in the second Test). But I didn't know he wasn't playing until the warm up."
It is understood medical staff had attempted to get Smith right, but ultimately he made the call that he wasn't quite there.
Smith's absence, combined with Pat Cummins' decision to bowl first as South Africa reached 0-140 at lunch, made for one of Australia's most dramatic mornings.
Of course, drama at Cape Town is nothing new for Smith or Australia.
This was meant to be his first Test at Newlands since the 2018 ball-tampering scandal, which ultimately cost him the captaincy and a year of international cricket.
There were some reminders of it on Tuesday, with the odd signs referencing sandpaper spotted in the Newlands stands and hills.
At age 37, Smith is also unlikely to come back for another Test, albeit with Australia's away tour schedule unknown beyond next year.
He has endured a frustrating tour with three scores in the 20s, while being hit in the head in Durban and then suffering the neck issue last week.
But his absence will be felt in a shaky batting line up, which will now have Cameron Green at No.4 and Josh Inglis at No.5 with Matt Renshaw opening.
"He is huge, one of the greatest batters we have ever had," Cummins said on Monday.
"You don't play 100-odd Test matches without playing Test matches where you're not 100 per cent fit.
"Even though he is probably not going to be 100 per cent hopefully he can compartmentalise that, like he has done a hundred times before with other things, and come out and contribute like he does every week."
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