The left-handed opener had courted controversy following the tourists' 231-run defeat in the second Test after accusing the South Africans of ball tampering, and the aggressive opener was the centre of attention once again at Newlands on Saturday.
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His fluent 135 helped Australia to 3-331 at the close, with captain Michael Clarke making a notable a contribution for the first time in the series with an unbeaten 92, well backed up Steve Smith (50 not out).
Warner, Clarke and Smith allowed Australia to set a platform that should enable them to go well past the 400 mark on day two, and there was further worry for the home side, who saw premier strike bowler Dale Steyn (1-44) leave the field nursing a hamstring injury.
Clarke copped a barrage of short-pitched bowling but bravely remained 92 not out. Photo: Getty
After winning the toss, Clarke opted to bat and Warner and Chris Rogers provided a solid start before the latter was caught at first slip by Graeme Smith off Steyn for 25.
Warner continued to play his shots in typical fashion as the visitors reached 118-1 at lunch, but Alex Doolan was dismissed shortly after the interval, caught at midwicket after mistiming a pull off Vernon Philander (1-66).
That brought Clarke to the crease, and the skipper endured a torrid time initially, twice receiving treatment after being struck by Morne Morkel (0-69), once on the forearm before a particularly nasty-looking blow that caught the batsman just under his left ear.
Warner had already brought up his seventh Test century by then, with a pulled four down to fine leg as the opener reached his milestone from just 104 deliveries.
After reaching tea at 2-195, the hosts finally ousted Warner, caught behind off JP Duminy (1-37), leaving Clarke and Smith to see Australia through to a significant position of strength at stumps with an unbroken stand of 114.