Warner made 51 off 79 balls as he batted with characteristic haste, running quick singles and hitting boundaries with expert placement as he put together a 56-run partnership with captain Steve Smith after Australia were reduced to 39-2.
Warner was caught at second slip by AB de Villiers off Vernon Philander in a blow for Australia, who looked to be steadying their innings following the early loss of Cameron Bancroft and Usman Khawaja on humid day in the coastal city.
Smith, coming into the four-test series ranked as the best batsman in test cricket and on the back of a prolific scoring run in the Ashes, will resume on 24 not out with Shaun Marsh due to join him out in the middle.
Smith had won the toss and showed little hesitation in opting to bat.
However, his hopes of a strong start soon evaporated when 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 wicketkeeper Quinton de Kock.
De Kock then took a flying catch to his left to snag Khawaja for 14 in the 12th over as the rangy Kagiso Rabada sent down just his fourth ball of the day.
South Africa will rue wasting both their allocated reviews early with Morne Morkel's insistence persuading a reluctant captain Faf du Plessis to check replays in the first over when Bancroft looked to have been trapped leg before wicket.
The hosts reviewed again when spinner Keshav Maharaj's first delivery caught Warner on his back leg but the DRS system showed the umpires were correct in ruling not out on both occasions.
(Reporting by Mark Gleeson in Cape Town; Editing by John O'Brien)
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