Sri Lanka won a dead final rubber by 112 runs under the D/L method in Colombo, as India took the series 3-2.
Opting to bat, the Sri Lankans lost Sanath Jayasuriya for one in the second over and as Kumar Sangakkara also fell for a single in the 19th it was 82-4.
An unbroken stand of 94 in 78 balls by Jehan Mubarak and Thilan Thushara, the latter hitting 54, helped muster 227-6.
India lost eight wickets for 33 runs in 12 overs and were all out for just 103, their worst total in Sri Lanka.
India were already struggling at 70-3 in the 15th over when an 80-minute delay for rain meant that their target was revised to 216 in 44 overs.
Seamer Nuwan Kulasekara unsettled the top order by bowling an impressive line and he recorded a career-best 4-40.
Spin wizard Ajantha Mendis bowled Yuvraj Singh with his first delivery and wrapped up the match with a haul of 4-10.
"It was a good way to finish the series, but the Indians played well and deserved to win it," said Sri Lanka skipper Mahela Jayawardene, who won his first toss of the series and chose to put runs on the board.
Reflecting on his team's failings earlier in the series he added: "We kept making mistakes throughout and were not consistent in the batting department.
"Credit goes to the boys for the way we came back in this match."
Counterpart Mahendra Dhoni chose to gloss over his team's slump in the final match, preferring to highlight the batting successes of previous games.
"These tracks are said to be slow, but the bounce has improved over the last few years," he commented.
"I am happy with the way our batsmen have played the spin. It was important to keep the strike rotating and our batsmen did that well."
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