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The 28-year-old was grit personified in a tension-filled fifth and final day, compiling an unbeaten 110 to steer the Proteas to safety at the Adelaide Oval.
Australia paceman Peter Siddle and spinner Nathan Lyon captured late wickets to leave South Africa wobbling at 240 for eight, but all-rounder Du Plessis and Morne Morkel survived the drama-filled final overs to leave the series tied at 0-0 after the drawn first test in Brisbane.
South Africa was 248 for eight at the close, 182 runs behind the 430-run target Australia captain Michael Clarke set for victory, with Morkel unbeaten on eight.
The third and final test starts in Perth on Friday.
"Faf was outstanding to make a 100 on debut," Clarke said.
"It's disappointing we didn't win the test ... but we've got to get up for Perth."
Du Plessis and Kallis seemed set to frustrate the hosts again after scoring a big partnership in the first innings, but Lyon struck to have Kallis caught for 38.
Siddle raised the tension by dismissing Dale Steyn for a duck for the seventh wicket.
Exhausted but charging in on pure adrenaline, Siddle bowled Rory Kleinveldt with a yorker to spark a roar from the spectators, but Morkel proved rock solid at the close and scored a pair of boundaries to defuse the threat in the final over.
Siddle earlier bowled AB de Villiers with a stinging off-cutter through the gate to remove the wicketkeeper for 33 and end the fifth-wicket partnership after a marathon 68 overs that started shortly after tea on day four.
Australia was frustrated twice by referral decisions, after Clarke had Du Plessis trapped in front immediately before and after the drinks break.
Both were given out and both decisions overturned on video review by the batsman.
The first review showed the ball pitching slightly outside leg stump before cannoning into Du Plessis' pad, while the second showed the ball had never touched the all-rounder's leg and had actually deflected off his bat.