Virat Kohli and Shubman Gill inspired India with the bat before Mohammed Siraj dismantled Sri Lanka in a thumping 317-run victory.
India had already wrapped up the series heading into the third and final ODI at Greenfield International Stadium in Thiruvananthapuram on Sunday.
Yet they made sure of a whitewash with a stunning performance with both bat and ball, as Sri Lanka endured a dismal day, with Ashen Bandara and Jeffrey Vandersay having to be taken off on stretchers.
After captain Rohit Sharma fell for 42, Gill (116) and Kohli (166 not out) put on a second-wicket partnership of 131 to pave the way for victory.
Gill succumbed to Kasun Rajitha (2-81) in the 34th over, having plundered 16 boundaries, but Kohli stayed in place throughout India's innings, striking eight sixes and 13 fours in a sublime knock.
Support came from Shreyas Iyer (38) as India set Sri Lanka, who lost both Vandersay and Bandara after the pair collided with each other in the field, a target of 391.
With only nine wickets to play with, the odds were stacked against the tourists, and Sri Lanka's slim hopes were over when Siraj (4-32) ripped through their top order.
Nuwanidu Fernando (19) was their top scorer, with Kasun Rajitha remaining unbeaten on 13 as Mohammed Shami (2-20) and Kuldeep Yadav (2-16) finishied the job for India.
Kohli lets rip to close in on Tendulkar
It was a magnificent knock by Kohli, who scored 113 in the first ODI of the series and ended it on a high note.
Kohli, who was playing against Sri Lanka in an ODI for the 50th time, now has 46 hundreds in the 50-over format, three short of the tally of India great Sachin Tendulkar.
His unbeaten 166 came from 110 deliveries, while his eight sixes marked the most he has struck in a single innings across all formats of international cricket.
Record up for India
India have now won 96 ODIs against Sri Lanka.
That means they have set a new record for the number of wins against a single opponent, surpassing Australia's total of 95 victories against New Zealand.