Fans paid tribute to retiring legend Jacques Kallis on his final Test.
Shikhar Dhawan was dismissed by Morkel after getting off to a good start and scoring 29 runs.
Morne Morkel was one bowler who kept the batsmen guessing throughout. He removed Dhawan early just when he was starting to look dangerous.
Pujara was yet again in the middle of an important partnership, this time with Murali Vijay. He went on to score an unbeaten half-century and take India to 181 for the loss of one wicket at the end of day one.
Murali Vijay did survive some important spells in the first Test but only this time did he convert it into a big score. He is unbeaten on 91 and on the verge of scoring his first overseas hundred.
Umpire Steve Davis stopped play for bad light almost two hours of play remaining.
Ajinkya Rahane played yet another responsible knock but was unlucky to miss out on a century.
South Africa picked up the key wickets of Cheteshwar Pujara and Virat Kohli very early in the day as the visitors were looking to salvage a draw.
It was a fitting farewell for arguably the greatest all-rounder the game has ever seen as he scored a hundred under pressure and also won the man of the match award.
South Africa pose with the trophy after crushing India by ten wickets.