The South Africans are already 1-0 up in the three-Test rubber, having won the opener by 72 runs in Cape Town.
"Ideally‚ we would not have liked to lose those wickets in the third session but it is part of the game and we remain positive‚" he said‚ adding that it was tough facing Indian spinner Ashwin who was assisted by the slow pitch.
It is ironic that one of the three chances India's fast bowlers created all day long was for a catch down the leg side, which, of course, was dropped by the wicketkeeper, playing this match because of a late hamstring niggle to the first-choice wicketkeeper, whose batting happens to have not looked good against pace and bounce in the last Test.
What helped Kohli most though was his running between the wickets as India motored on despite not taking many risks. South Africa's score then was 282 for 7.
Rohit Sharma (10) continued to fail for the third consecutive innings as he was ruled LBW against Rabada. It looked out to the naked eye and the umpire duly confirmed those suspicions, but Sharma went upstairs for the review.
Patel had put on 32 runs with Kohli for the fifth wicket but became Ngidi's maiden Test wicket just as the innings started to look stable. Amla who'd joined him had some luck go his way when Hardik Pandya missed a hard chance at short midwicket, but otherwise the veteran no.3 look composed.
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.
Morne Morkel struck shortly after lunch when he removed KL Rahul for 10, hanging onto a brilliant catch off his own bowling.
Vijay too had a couple nervy moments against Vernon Philander but managed to survive the spell.
India then ventured into the Proteas' comical territory. "We made a very good comeback on the first day evening when (Hashim) Amla got run out and we got six wickets (in the day)", Jaffer told reporters here on sidelines of an event in Mumbai. "If I am ready to take those important wickets for the team, I am always up for it", Ishant said when asked about his absence from the first Test.
"To have them five down at the end of the day, we'll take that position any day", said South Africa quick bowler Lungi Ngidi, who is making his test debut.
Ashwin and Sharma were the two outstanding bowlers for the Indians; with the off-spinner picking up 4/113 in 38.5 overs, while Sharma, who replaced Bhuvneshwar Kumar, claimed 3/46 in 22 overs.
They got their first wicket of the day thanks to Mohammed Shami.
India could have made further inroads following Maharaj's dismissal but Kohli dropped Rabada off Ashwin at slip, only managing get his right-palm under the ball but unable to hold on to it.
Credit has to go to Hardik Pandya for changing direction in his follow-through, fielding a ball nearly at square leg, turning around and going for and achieving a direct hit at the end that the batsman - Hashim Amla, slower of the two at that time - didn't expect action.
Earlier, South Africa skipper Faf du Plessis played a similar role to Kohli with a precious half-century to take his team past 300.