Sri Lanka scored a consolation win after losing three matches in trot and the Idea Cup to the tourists.
However, the margin of victory was more than convincing as the Indians conceded 112-run loss in the fifth and final one-dayer played on Friday.
India were bowled out for 103 after rain reduced their target from 228 to 216 in 44 overs, with fast bowler Nuwan Kulasekera and spinner Ajantha Mendis sharing eight wickets.
Dhoni was adjudged man of the series for his contribution with the bat in the tournament. He scored 193 runs with two half centuries in the series.
The four previous bilateral one-day series played by India in Sri Lanka had ended in the host country winning two and drawing two.