India were 50 for 2 in 15 overs with Cheteshwar Pujara (19) and skipper Virat Kohli (15) at the crease when the match officials declared early lunch break.
Sri Lankan pace bowlers made an impact straighaway after inviting the visitors to bat on a recently laid grassy pitch as they got rid of Rahul (2) in the second ball of the day.
Dhammika Prasad (1/16) bowled an inswinger that jagged back massively and the bamboozled young opener saw his stumps shattered.
Rahane (8) started off with a couple of crispy drives down the ground but his stay did not last long either as he was struck in front of the legstump by Nuwan Pradeep (1/16) in the fourth over and was out plumb LBW.
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With both centurions from the second Test back in the pavilion, India were struggling at 14/2, as Kohli walked to the crease.
The India captain was lucky to be still batting when the rain-break came. In the eighth over he was dropped off Pradeep by Perera who is keeping instead of Dinesh Chandimal.
Later, Prasad went off the field with a sore back. Angelo Mathews bowled a few overs as India were placed at 40 for 2 after the first hour's play. Rangana Herath also bowled an over, before rain came down in a hurry.
India made two changes to the playing eleven, with Pujara coming in for the injured Murali Vijay, and Naman Ojha was handed his Test debut. He replaced injured Wriddhiman Saha.