Smith, who had been prolific with the bat in leading Australia to success in the Ashes, scored 56 before feathering a bottom edge off spinner Keshav Maharaj that went through to strike wicketkeeper Quinton de Kock on the shoulder and pop up for AB de Villiers to take the catch.
It was the only wicket for the hosts in the second session after David Warner fell for 51 with the last ball before lunch.
Smith offered a chance to de Villiers off Vernon Philander when on 47 but the South African slip could not hold on, allowing him to go and reach his 24th test 50.
The Australia captain featured in 56-run partnerships with both Warner and Shaun Marsh after winning the toss and looking to take advantage of a slow wicket in hot and humid conditions.
Marsh (34) and his younger brother Mitchell (8) were not out at tea.
Warner made 51 off 79 balls as he batted with characteristic haste, running quick singles and hitting boundaries with expert placement to steady Australia's innings after they were reduced to 39-2 in the 12th over.
Australia opener Cameron Bancroft was dismissed in the sixth over for five as he shuffled down the track to a delivery from paceman Philander and got a thick edge through to de Kock, who then took a flying catch to his left to snag Usman Khawaja for 14 as the rangy Kagiso Rabada sent down just his fourth ball of the day.
(Reporting by Mark Gleeson in Cape Town; Editing by Pritha Sarkar)
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