The visitors, however, surrendered some of the advantage and lost opener Stiaan van Zyl for a duck to off-spinner Ravichandran Ashwin and nightwatchman Imran Tahir (four) to Ravindra Jadeja to slump to 11-2 at stumps.
Dean Elgar (seven) and captain Hashim Amla (nought) were unbeaten at the crease with South Africa, who trail the four-test series 1-0, still 204 runs behind.
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 strikes from Morkel and Harmer, who returned to the side after playing the opening test in Mohali, eroded most of the advantage the hosts thought they had by batting first.
News that makes sense
Your trusted source for staying up-to-date with the world around you. Get free daily news updates and analysis, straight to your inbox.
Jadeja (34) and Wriddhiman Saha (32) then combined in a crucial 48-run stand to ensure the hosts had a competitive total in what appears to be a low-scoring match after India were reduced to 125-6 at one stage.
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 series.
It will not be an easy task for South Africa, especially on a track which has already seen spinners from both sides claim eight out of the 12 wickets to fall on the opening day.
Part-time left-arm spinner 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), India's top scorer, looked in control 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 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.
Harmer sent back Cheteshwar Pujara (21) and Rohit Sharma (two), who was playing his first match in the series, before also dismissing Saha who was caught acrobatically by JP Duminy at short mid-wicket.
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.
(Reporting by Sudipto Ganguly in Mumbai; editing by Amlan Chakraborty)
