Steady showers had allowed just 11.5 overs on the first day of the three-match series and the heavens opened once more on Friday to initially force an early lunch and then wash out the final two sessions with India reeling on 74 for five.
When play was called off, Pujara, a model of concentration, stood three runs short of a 16th test fifty, a knock he would be proud of considering the conditions at Eden Gardens.
Local favourite Wriddhiman Saha survived some anxious moments to remain six not out at the other end as the visitors continued to plunder wickets between the showers in search of a first test win against their hosts in India.
Sri Lanka's first change bowler Dasun Shanaka dismissed Ajinkya Rahane and Ravichandran Ashwin, both for four, to compound India's woes after the hosts had resumed on 17-3 under an overcast sky.
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Suranga Lakmal had claimed three wickets on the opening day without conceding a run and the paceman eventually sent down 46 dot balls before Rahane hit a boundary to end the streak.
Shanaka struck in his third over when Rahane chased a wide delivery and nicked a catch to wicketkeeper Niroshan Dickwella.
Next man in Ashwin was hit on the thumb by a rising Lahiru Gamage delivery and needed medical attention, before he also fell victim to a very ordinary shot against Shanaka, slicing a delivery straight to Dimuth Karunaratne at point.
Saha looked tentative as well but Pujara batted with characteristic assuredness at the other end.
On a green track where the ball moved significantly, Pujara came up with a batting masterclass -- playing late, close to his body with soft hands and leaving well.
India's number three was his watchful self against anything outside the off stump and capitalised on the occasional poor delivery, as the nine boundaries in his 102-ball vigil would suggest.
(Reporting by Amlan Chakraborty in New Delhi; Editing by John O'Brien)
