Pujara was batting on 122 and Virat Kohli, who struck a century in the first innings, on 77 and the duo with their 191-run stand for the third wicket, took India to 282 for two in the second innings at stumps for an overall lead of 320 runs.
Pujara struck 18 fours in his 221 ball knock while Kohli hit eight fours during his 132-ball stay.
The day completely belonged to India and the injury to pacer Morne Morkel, who twisted his ankle while fielding, only made things worse for the Proteas. Morkel has been ruled out of the Test with a grade one ligament injury.
If it were the Indian pacers, Zaheer Khan and Ishant Sharma, who struck earlier in the day to bowl out South Africa for 244 runs in the first innings, the batsmen stole the limelight later in the day.
With a 36 runs lead, India lost opener Shikhar Dhawan (15) early after he became fast bowler Vernon Philander's 100th Test victim, caught at second slip by Jacques Kallis with the score at 23/1.
Murali Vijay (39) and Pujara took India to a position of strength with their 70-run stand for the second wicket.
South African bowlers once again adopted their negative approach of bowling well outside the off-stump and the Indian batsmen were more than happy to leave them alone.
Pujara and Vijay showed great levels of patience and kept the South African pacers at bay as India took a 145-run lead by the tea break. Vijay, however, was unlucky to be dismissed, poking at a delivery outside the leg-stump and getting a faint edge shortly before the tea break.
Pujara and Kohli scored at will as runs flowed freely in the last session of the day, when 175 runs were scored. Pujara got his ton with a sumptuous drive through the covers for four off Dale Steyn. He punched the air as his team mates cheered him from the dressing room.
Earlier in the day, inspired performances by pacers helped India take a first innings lead of 36 runs after bowling out South Africa for 244.
Sharma (4/79) registered his best figures on South African soil and Zaheer(4/88) made a sensational return to international cricket after 12 months as South Africa suffered their second batting collapse. Mohammad Shami got two for 48.
South Africa, who lost five wickets for 16 runs on the second day, lost another flurry of wickets on the third day in their first innings. Resuming at 213/6, they lost the last four wickets for 31 runs. Overnight batsmen Vernon Philander made 59 and Faf du Plesis made 20.
Philander's knock was ended by Zaheer who pitched it outside the off-stump, short of length, and the edge flew to Ravichandran Ashwin at first slip.
Dale Steyn (10) smacked two consecutive fours off Zaheer but was removed by Ishant, who ducked it short as the South African tried to fend it away but only managed to edge it to Rohit Sharma in the slips.
Zaheer struck again in the next over to dismiss Du Plesis, caught behind by Mahendra Singh Dhoni and then went on to wrap up the innings with a yorker to castle Morne Morkel.
--IANS (Posted on 21-12-2013)