Dhoni failed to hit a winning boundary off the last ball by Lasith Malinga, leading both teams to finish level at 236 for nine off 50 overs.
Dhoni, who won last Sunday’s ODI against Australia in the final over, came close to repeating that success but his swipe over extra cover was cut off, and the last two Indian batsmen scampered through for three runs.
Dhoni was named man of the match with his unbeaten 58 off 69 balls and two catches in Sri Lanka’s innings.
The two points lifted India to the top of the tri series standings ahead of Australia with Sri Lanka still yet to win in their three games.
Match scores: Sri Lanka 236 for 9 (50 overs), India 236 for 9 (50 overs).
Scoreboard
Sri Lanka
U Tharanga c Dhoni b Vinay Kumar 0
T Dilshan c Dhoni b Pathan 16
K Sangakkara c Gambhir b Ashwin 31
D Chandimal run out (Sharma) 81
M Jayawardene lbw b Vinay Kumar 43
A Mathews run out (Dhoni) 17
T Perera c Kohli b Ashwin 5
N Kulasekara c Gambhir b Vinay Kumar 12
S Senanayake not out 22
L Malinga run out (Raina) 0
R Herath not out 1
Extras (lb3, w5) 8
Total (9 wickets for; 50 overs) 236
Fall of wickets: 1-0 (Tharanga), 2-28 (Dilshan), 3-79 (Sangakkara), 4-173 (Jayawardene), 5-178 (Chandimal), 6-184 (Perera), 7-210 (Mathews), 8-232 (Kulasekara), 9-235 (Malinga)
Bowling: Vinay Kumar 10-1-46-3 (1w), Pathan 9-0-38-1 (2w), Yadav 9-0-51-0, Ashwin 10-1-30-2, Jadeja 10-0-58-0, Sharma 2-0-10-0 (2w)
India
G Gambhir run out (Kulasekara) 91
S Tendulkar c Sangakkara b Kulasekara 15
V Kohli lbw b Perera 15
R Sharma run out (Jayawardene) 15
S Raina c Sangakkara b Malinga 8
MS Dhoni not out 58
R Jadeja c Jayawardene b Perera 3
R Ashwin c Senanayake b Malinga 14
I Pathan run out (Mathews) 8
R Vinay Kumar run out (Mathews) 1
U Yadav not out 0
Extras (lb1, w6, nb1) 8
Total (9 wickets for; 50 overs) 236
Fall of wickets: 1-24 (Tendulkar), 2-61 (Kohli), 3-94 (Sharma), 4-118 (Raina), 5-178 (Gambhir), 6-184 (Jadeja), 7-212 (Ashwin), 8-223 (Pathan), 9-233 (Vinay Kumar)
Bowling: Malinga 10-1-53-2 (1w/2), Kulasekara 10-0-39-1 (1w), Mathews 5-0-35-0 (1nb, 1w), Perera 9-0-45-2 (1w), Herath 10-1-33-0 (1w), Senanayake 6-0-30-0
Match tied
Man-of-the-match: M.S. Dhoni (IND)
Toss: Sri Lanka
Umpires: Simon Fry (AUS) and Nigel Llong (ENG)
TV umpire: Bruce Oxenford (AUS)
Match referee: Andy Pycroft (ZIM)
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