India are now 107 runs ahead with three days' play left in the match.
The tourists now stand at 21/1 at stumps, trailing by 384 runs.
Dimuth Karunaratne, on 11, and Lahiru Thirimanne, on 9, were at the crease after paceman Ishant Sharma bowled Sadeera Samarawickrama for 0 with the second ball of the innings.
The day ended with Pujara and Virat Kohli unbeaten on 121 and 54 respectively.
"I think it's his confidence".
It was the star batsman's fifth 200-plus score in his 62nd Test.
At the time of reporting, India were 456 for four, with Rohit Sharma batting at 19 and Kohli at 143.
Kohli's all double hundreds have come against different oppositions. 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.
"I think it was hard to score runs as this wicket was on the slower side".
Twice former Australian captain Ricky Ponting had hit nine hundreds across two formats in 2005 and 2006, while former South Africa skipper Graeme Smith also had nine global hundreds to his credit once.