Pujara and Kohli have added 191 runs in the third wicket partnership so far, taking the visitors to an advantageous position in the match after they were defeated 2-0 in the ODI series earlier.
Earlier in the day, Indian bowlers cleaned South Africa's tail as the hosts were all out at 244 runs, trailing India's first innings score of 280 runs by 36 runs.
In the second innings India lost opener Shikhar Dhawan (15) with just 23 on the scoreboard.
Jacques Kallis broke the small partnership of 70 runs posted by Murali Vijay (39) and Pujara by picking up the wicket of the India opener.
South Africa, however, received a jolt as they lost pacer Morne Morkel to an ankle injury early in the Indian innings.
With regular spinner Imran Tahir giving away 55 runs in his 11 overs without picking up a wickets and pacers struggling to break the partnership between Kohli and Pujara, South African skipper
Graeme Smith tried seven bowlers, including wicket-keeper AB de Villiers, with hopes of testing some success and returning back to the game which has been dominated by India so far.
Experienced Indian fast bowler Zaheer Khan picked up three wickets on Friday morning and Ishant added one more wicket to his name bowl out South Africa for 244.
Both Zaheer and Ishant picked up four wickets each in the game while Mohammed Shami bagged two.
India were 280 all out in their first innings with Kohli top scoring for the home side with his 119.
India- 280, 284 for 2 in 78 overs (C Pujara 135*, V Kohli 77*, J Kallis 1-51, V Philander 1-53)
South Africa- 244 all out
--IBNS (Posted on 20-12-2013)