After winning the toss, Rahul said Kohli is out due to upper-back spasm and Hanuma Vihari comes into the playing eleven.
Quinton de Kock smashed some boundaries while sharing a stand of 31 with Bavuma before chopping on to his stumps while trying to cut off Siraj.
The hardworking Siraj bowled one with the scrambled seam and just like the first innings, tried to cut with very little room for execution with the ball coming into him.
Earlier, Rahul and Mayank Agarwal justified captain Kohli's decision to bat first with a careful yet solid opening stand as India reached 83/0 in 28 overs at lunch.
Harbhajan, who made his India debut during an ODI against New Zealand at Sharjah in 1998, last played for the country in March, 2016 during a T20I against the UAE at Dhaka.
While injured Rohit Sharma will miss the Tests in South Africa, the ODIs after that will see Kohli being unavailable for the Indian team.
He is also now three runs away from overtaking former Australia captain Ricky Ponting's 2005 haul of 1544 runs.
"That's an honest truth and I am grateful for having a big presence in a country that is so far away from my home." said the former West Indies all-rounder Dwayne Bravo.
A total of 45 matches will be played across seven venues in Australia between October 16 and November 13 next year.
New Zealand's hopes now rest with Nicholls (36 not out) and Rachin Ravindra (2 not out) as they survived the few overs remaining for the day. Ravindra, who had denied India victory in the first Test at Kanpur holding the fort with last man Ajaz Patel, would be hoping to do the same but this time India has too much time left in their hands and New Zealand too few wickets.
"The stars have aligned for me to do it in Mumbai," New Zealand spinner Ajaz Patel said Saturday said after achieving the rare feat of scalping all 10 batters in an innings at the city of his birth.
The whole cricket fraternity heaped praise on Patel for his stupendous feat of taking all 10 wickets in an innings of a Test match. Most of them termed the feat as an ‘unreal’ and a ‘special effort’.
India are now scheduled to play three Tests and three ODIs during the tour, which will start with the first Test in Johannesburg on December 17.
Resuming the day at 221 for four, India scored 64 runs in the morning session with the loss of two wickets.
The release puts to rest speculation of likely tough selection calls being taken by the team management in the wake of below-par performances from Ishant Sharma and Ajinkya Rahane in the opening Test at Kanpur.