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Virender Sehwag (13) and Rahul Dravid (5) were both dismissed cheaply as India reached 49 for two at tea.
Kallis was the mainstay of the South African innings, making 161 before being last man out. Kallis batted superbly with tailenders Paul Harris and Lonwabo Tsotsobe, taking his score from 100 to 161 while the last two wickets added 79 runs.
It was the South African batting star’s 39th Test century, moving him into joint second place on the all-time Test centurions list alongside Ricky Ponting of Australia and behind only India’s Sachin Tendulkar, who has made 50 hundreds.
It was also the highest of seven Test centuries by Kallis at Newlands, his home ground.
The innings came at a cost to South Africa, however, as Kallis aggravated a side strain while batting and did not take the field at the start of the Indian innings.
Sehwag again had a disappointing first innings after being out for nought in the first Test in Centurion and 25 in the second match in Durban. He made 13 before a typically flat-footed drive against Dale Steyn spooned to mid-off where South African captain Graeme Smith made a good catch, diving forward.
Dravid was out in unusual circumstances when Gautam Gambhir was dropped on 10 by Alviro Petersen at gully off Tsotsobe. The batsmen went through for a run but second slip AB de Villiers picked up the ball and threw down the stumps with Dravid just short of his ground.
South Africa’s eventual total seemed unlikely when they lost four wickets in the space of 26 balls against the second new ball during the first hour of the day. Three of the wickets fell to fast bowler Shanthakumaran Sreesanth, who finished with five for 114. It was Sreesanth’s third five-wicket haul in Tests.
Sreesanth struck in his first over of the day, after Kallis and Ashwell Prince had added 30 runs to the overnight total of 232 for four. Prince looked in particularly good form as he moved to 47 before being bowled by a ball from Sreesanth which cut back sharply.
Sreesanth had Mark Boucher caught behind off the next delivery, Zaheer Khan had Dale Steyn caught at third slip and Sreesanth had Morne Morkel caught behind.
Paul Harris helped Kallis add 27 for the ninth wicket and Kallis then gave a masterly exhibition of keeping the strike as he and Tsotsobe added 52 for the last wicket before Kallis edged an attempted square cut against Zaheer Khan in trying to keep the strike yet again.
Kallis reached a watchful century off 209 balls but scored his next 61 off only 82 deliveries, adding ten more boundaries to the nine in his first 100.
