India captain Virat Kohli had no hesitation in opting to bat first after winning the toss at the VCA Stadium with the pitch expected to assist the slow bowlers.
But three wickets from the lanky paceman eroded most of the advantage the hosts thought they had by batting first.
Ravindra Jadeja (21) and Wriddhiman Saha (nine) added 24 runs in an unbroken stand before the break after South Africa had reduced the hosts to 125-6.
The surface provided prodigious turn for the spinners from the first session of the match, which the touring side, currently the top-ranked test team, need to win to level the four-match series.
Part-time left-arm spinner Dean Elgar broke India’s opening stand by dismissing Shikhar Dhawan (12) after the left-hander had added 50 with Murali Vijay.
Dhawan advanced down the wicket but could only manage to spoon the ball back to the bowler, who took a smart diving catch.
Vijay (40) looked in control during his knock before he was done in by a Morkel delivery that straightened after pitching to hit the batsman plumb in front of the wicket.
Morkel, leading the South African pace attack in absence of injured team mate and world’s top-ranked test bowler Dale Steyn, beat Kohli (22) several times before inducing an edge from the right-hander which was pouched by wicketkeeper Dane Vilas.
Ajinkya Rahane (13) struggled throughout his stay at the crease and played an expansive drive off Morkel to be clean bowled.
Off-spinner Simon Harmer further pegged India back by dismissing Cheteshwar Pujara (21) and Rohit Sharma (two), who was playing his first match in the series.
Both sides went in with an extra spinner for the match with India opting for leg-spinner Amit Mishra and South Africa adding Harmer to their line-up.