Kohli was joined by Ajinkya Rahane for a short period as the right-handed batsman departed for just 2 after handing out a catch to Dimuth Karunaratne on Thisara Perera's ball.
India are now 107 runs ahead with three days' play left in the match.
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After the early departure of Rahul on day one, Murali Vijay (128) and Pujara had put India in the driving seat with their 209-run second-wicket partnership.
On the second day's play, Captain Virat Kohli (54 not out) along with Pujara were on the crease. "And the way he is batting in the last two-three years, it would have been hard for any other batsman to score with such a strike rate", Pujara told reporters. He has also achieved double centuries against the West Indies, New Zealand, England and Bangladesh.
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At the time of reporting, India were 456 for four, with Rohit Sharma batting at 19 and Kohli at 143. He found able support in the form of Cheteshwar Pujara who remained unbeaten at stumps with a century of his own. He gave nothing away and brought together his fourth Test century this year and became the third batsman to 1000 Test runs (1046 runs). Following that, Vijay and Pujara took a cautious approach and started to build the Indian innings.The duo opted to wear out the Lankan bowlers in the first session and hit the occasional boundaries to keep the scoreboard ticking.
Australia's Ricky Ponting had hit nine hundreds across two formats in 2005 and 2006, while South African Graeme Smith once had nine centuries to his credit.
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