Resuming the session at 78/0, South Africa quickly lost experienced left-handed batsman Elgar, who stepped out of the crease but his uppish drive to a rising delivery from Ashwin went to close-in fielder Murali Vijay.
South Africa profited with what could be crucial first innings runs through this period, before Rabada was superbly caught by, ironically, Pandya at deep mid-wicket as he attempted a hook off the excellent Ishant Sharma (3-46).
Those strikes went a long way in turning a day of toil into a position of parity for India, and lifted their mood after two sessions of largely ineffective bowling barring R Ashwin's two wickets.
Du Plessis earlier in the morning won the toss and elected to bat on a bouncy wicket with less seam and swing as compared to the Newlands wicket in the first Test.
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Patel was playing in place of Wriddhiman Saha, who had a hamstring injury. Another change was Lokesh Rahul replacing Shikhar Dhawan.
Even Ashwin wasn't spared as the South Africa skipper swept him for a boundary behind deep backward square leg. The post-lunch session promises to be interesting.
And the way the South Africans started their innings, it appeared things were going to get really worse for the Indian team as Dean Elgar and Markram looked largely unperturbed against the fast bowlers from the visiting team.
The third session was fruitful for the Indians as they claimed the key wickets of Amla, AB de Villiers (20).
Amla and De Villiers had scored 51 for the third wicket; South Africa's third successive half-century partnership of the day.
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The Poland star is returning to full training after a knee injury, but Heynckes opted to start Thomas Mueller up front for Bayern. Dominik Kohr's 18th minute header narrowly missed the target but was their best chance before Bayern gradually took control.
It got worse for South Africa when Vernon Philander set off for a suicidal run and found himself at the same end as Du Plessis to be run out without scoring.
Pandya made the pick-up off his own bowling, turned and ran Amla out.
Making a pronounced movement across his stumps - much as he had in Cape Town - Vijay played at a greater percentage of balls in this channel than he is known to, particularly early in his innings, but looked in control apart from a couple of plays and misses.
In the very next over, Quinton de Kock (0) was caught at slip by Virat Kohli off Ashwin. After playing a Pandya delivery towards the short midwicket, Philander ran towards the other end without a confirmed approval from du Plessis.
Brightline to begin serving passengers January 13
Brightline has not released monthly pass prices for its trains yet, nor has the company said when the introductory fare will end. Officials tell local news outlets the company will make 10 round trips daily and nine trips on weekends.