India had been fretting over the first-down position after Sai Sudharsan, one of the seven batters tried in that position in the last two years, was ruled out with a toe injury.
It opened the door for Padikkal, and the left-hander responded with a free-scoring 131 not out on Saturday, putting India on course for a formidable first-innings total on the opening day at the Galle International Stadium.
Opener KL Rahul had earlier made a composed 77 before retiring hurt.
India got off to a fluent start after captain Shubman Gill opted to bat first on a track that always promised plenty of runs.
Yashasvi Jaiswal and Rahul added 47 for the opening wicket before an almighty mix-up left both batters stranded at the non-striker's end.
Jaiswal (32) was run out, but Rahul joined forces with Padikkal in a 150-run stand that kept Sri Lanka wicketless through the rain-delayed second session.
Padikkal nearly offered a return catch to Sri Lanka captain Dhananjaya de Silva early in his innings but was otherwise the epitome of elegance.
Having opened his account with a boundary, the left-hander stepped out against Prabath Jayasuriya and lofted the left-arm spinner over his head for six.
Padikkal's aggression appeared to rub off on Rahul, who gave Jayasuriya similar treatment in the spinner's next over.
Padikkal brought up his half-century with a single off Lahiru Kumara, while Rahul soon reached his own fifty as the pair milked the Sri Lanka attack with consummate ease.
As the runs continued to flow, Rahul developed cramps and retired hurt after an assured knock featuring nine fours and a six.
Gill, who made 16, struck two sweetly-timed boundaries before throwing away his wicket. The right-hander charged at Jayasuriya, only to sky a catch to mid-off.
Rishabh Pant made a breezy unbeaten 27 and will look to continue his fine start when play resumes in India's 600th Ttest, and also the 50th Test at Galle.
