Smith was sidelined from fielding on Monday afternoon after being struck on the side of the helmet by Anrich Nortje while batting on the morning of day four.
He initially passed an on-field test and continued batting, but Australia's medical staff then planned to continue assessing him for any delayed symptoms.
However the vice-captain returned to complete warm-up drills on Tuesday morning, and took to the field in the slips as Australia pursued a series-opening victory.
Had Smith been diagnosed with a concussion the 37-year-old would have been in extreme doubt for the second Test starting Sunday in Gqeberha.
But his availability looms as crucial for Australia, particularly given South Africa are set to welcome back their strike weapon Kagiso Rabada.
It was in Gqeberha (formerly Port Elizabeth) that Smith and Rabada clashed during the dramatic 2018 series, when the fast bowler shouldered him after a wicket.
Rabada was initially suspended for the final two Tests of that series over the contact, but had the penalty downgraded to a fine on appeal.
That case overshadowed what was a brilliant series from the Proteas quick, who took 23 wickets at 19.26.
Smith made scores of 25 and 27 for Australia in Durban, but left his biggest mark on the match with three brilliant catches in the first innings.
Australia will have selection decisions to make for the second Test anyway, with Josh Inglis likely to be available again after his fractured finger.
But Nic Maddinson's quickfire 48 on Monday could be enough to keep him in the XI, given his selection as opener has allowed Matt Renshaw to score 190 and 82 at No.5.
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