Pujara played freely and without any hesitation on the final day of the match, finding the fence at will while maintaining a strike rate of over 100.
Ajinkya Rahane was suddenly dropped from the India ODI side despite a good run in the last couple of years.
Along with their batting unit's failure apart from Rishabh Pant and Virat Kohli, Cheteshwar Pujara dropped an easy catch.
Virat Kohli held firm but Rishabh Pant stole the show with a brilliant fifty to boost India against South Africa in Cape Town.
Cheteshwar Pujara and Ajinkya Rahane fell cheaply as India started badly on day 3 of the Cape Town Test.
The premier Indian fast bowler picked up a five-wicket haul to bowl out South Africa for 210 runs, allowing the visitors to take a 13-run lead.
Virat Kohli and Cheteshwar Pujara hit solid knocks but South Africa made consistent inroads on day 1 of the Cape Town Test.
Virat Kohli and Cheteshwar Pujara have steadied India after losing the openers against South Africa in the first session in Cape Town.
Harbhajan Singh hopes the team management will go ahead with former Test deputy Ajinkya Rahane for the third Test against South Africa.
Elgar remained unbeaten on 46 as South Africa need 122 more runs to level the Test series against India.