It is only the second match in India's 12-Test long overseas schedule in 2018-19, and already they are faced with a tricky situation in a bid to keep this series alive.
Du Plessis finished on 25 off 77 balls, which included three boundaries, while Maharaj remained undefeated on 10 off 23 deliveries, which included two boundaries.
Markram, who was raised just a few kilometres from the Centurion Park stadium, will resume after the interval on 51 along with a more cautious Dean Elgar, who has 26. He made 63 in just over three and half hours facing 142 balls and hitting nine fours.
Markram's timing was crisp, and in front of his parents and his home crowd in his city of birth, he looked like he could bat all day. A niggle in the hamstring for Wriddhiman Saha gave Parthiv Patel an opportunity with the glove.
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We really shouldn't be surprised that Virat Kohli made changes from the XI that lost at Newlands given that in his 34 Tests as captain he is yet to name the same team twice.
India would have been desperate to make further inroads at that stage to get back into the contest, but with Du Plessis and Amla ticking along comfortably, it didn't look likely. Pandya appeared to be distracted by the presence of KL Rahul and his frustration came out when he jumped up and down like a kid who'd been denied an ice-cream.
Markram edged a delivery from spinner Ravichandran Ashwin to wicketkeeper Parthiv Patel on 94 coming from 150 balls as he was denied a third test century in his seventh innings.
Quinton de Kock failed to trouble the scorers as he was dismissed for a golden duck after being caught by India captain Virat Kohli at slip off the bowling of Ashwin.
Had Amla and du Plessis not attempted a suicidal single, the day could have still belonged to South Africa, but there was hesitation in the calling when Amla had tapped Pandya on the legside, and the fleet-footed and sure-armed Pandya swooped in to get the ball and hit the stumps to leave Amla a yard short.
Pandya went short at Vernon Philander, who didn't look comfortable but somehow fended it off to a heavily-packed on-side field.