India have meanwhile started batting and are at 4-0 at lunch.
For his dismissal‚ Markram's review was unsuccesful as Ultraedge showed that the ball came off his bat and the decision remained that of the umpire‚ who originally had waved his finger for out.
Watch day two of the second Test between South Africa and India, live on Sky Sports Cricket (channel 404) and Sky Sports Main Event (channel 401) from 7.55am on Sunday. After India's humiliating failure to grab victory in the first Test against the Proteas side, Kohli was heavily criticized.
That took South Africa from 246/3 to 251/6, and what should have been a dominant day at the office became one that India will be more satisfied with. Philander looked to get off strike and was running towards the other end looking at the ball and not Faf Du Plessis.
Opener Aiden Markram (94), playing on his home ground, missed a well-deserved century by a whisker after he was caught behind off Ashwin (2-53).
After wickets fell in heaps in the first Test at Newlands, the pitch at SuperSport Park presented an entirely different proposition as batsmen ruled the roost. KL Rahul replaced Shikhar Dhawan at the top of the order in an expected move, while Parthiv Patel was handed the wicketkeeping gloves with Kohli informing at the toss that Wriddhiman Saha had a hamstring niggle. Elgar never looked comfortable but hung in, and even benefitted when he pulled Bumrah to square leg but M Vijay misjudged the path of the ball and took a couple of steps in, only to see it go over his head.
South Africa made only one change, handing a debut to the young quick Lungisani Ngidi in place of the injured Dale Steyn.
But the Indians struck soon after the lunch break as R Ashwin sent back Elgar, caught by Murali Vijay at silly point.
India had initially contained the home batsmen in the first 90 minutes of the session, bowling excellent lines that made scoring shots a risk. He is the seventh Indian pace bowler to achieve this distinction, behind Kapil Dev, Zaheer Khan, Javagal Srinath, Ishant Sharma, Karsan Ghavri and Irfan Pathan.
Du Plessis was at the centre of the next run-out, too, except this time he was the one not interested in a single. It was particularly satisfying for him to have contributed with the wickets of Dean Elgar, Aiden Markram and Quinton de Kock on a day that for a long duration looked like it was going ominously wrong for India.