Warner, who courted controversy after the second test by claiming the victorious South Africans had tampered with the ball, reached his fifty at a run a ball after Australia had won the toss and elected to bat. Teams: (Agencies)
He will resume after the interval on 70 along with Alex Doolan, who has 13, the pair sharing a 53-run second wicket stand.
The only wicket to fall in the opening session was that of Chris Rogers (25), who edged Dale Steyn to Graeme Smith at first slip when Australia had raced to 65.
There was clear intent from the tourists to attack the South African bowlers on a wicket that offered little in the way of sideways movement, with Warner the most brutal.
Both sides made two changes to their startling line-ups. South Africa restored batsman Alviro Petersen to their team after he missed the second test through illness. He comes in for Quinton de Kock, who debuted in Port Elizabeth.
Fast bowler Kyle Abbott wins a second test cap as a replacement for injured all-rounder Wayne Parnell, who misses out with a groin strain.
The 26-year-old Abbott made his test debut against Pakistan in Pretoria last February, taking nine wickets for 68 runs in the match, but when the Proteas returned to the test arena in October, was not selected.
For Australia, Shane Watson has passed a fitness test and makes his first appearance of the series after shaking off a calf injury, coming in for Shaun Marsh after the left-hander collected a pair of ducks in Port Elizabeth.
Paceman James Pattinson replaces Peter Siddle, having not played test cricket since the Ashes series in England in July last year.
Australia won the first test in Pretoria by 281 runs, but South Africa levelled the three-match series with a 231-run win in Port Elizabeth.
South Africa: Graeme Smith (captain), Alviro Peterson, Hashim Amla, Faf du Plessis, AB de Villiers, Dean Elgar, JP Duminy, Vernon Philander, Dale Steyn, Morne Morkel, Kyle Abbott.
Australia: Chris Rogers, David Warner, Alex Doolan, Michael Clarke (captain), Steve Smith, Shane Watson, Brad Haddin, Mitchell Johnson, James Pattinson, Ryan Harris, Nathan Lyon.
Warner, who courted controversy after the second test by claiming the victorious South Africans had tampered with the ball, reached his fifty at a run a ball after Australia had won the toss and elected to bat.