Dhoni, needing four off the last ball to reach the victory target of 237, slashed experienced paceman Malinga over cover but an outfielder's diving save cut off the boundary and India finished at 236-9 — the exact score Sri Lanka posted in 50 overs.
Dhoni finished unbeaten on 58, just failing to repeat his match-winning, last-over victory against Australia last weekend.
After plundering 15 off the 49th over from Angelo Mathews, India needed an achievable nine runs for victory off the last six balls. But with Malinga bowling, Sri Lanka was still in serious contention.
In a tense finish, Dhoni narrowly survived a run out three balls from the end when Malinga couldn't handle a throw over the bails from Mahela Jayawardene.
The result was the first tie between India and Sri Lanka in a limited-overs international, although both teams have featured among the 25 previous tied ODIs. India has been involved in six ties, including three in the last 12 months, and Sri Lanka has been involved in four ODI ties.
"Malinga is very difficult to hit so we were looking to target Mathews," said Dhoni, who was the hero of India's World Cup final win over Sri Lanka at Mumbai last April. The last shot "was a bit difficult here, but in India that would have been two bounces and four. When you need 10 or 12 in the last over your heart rate will always be up." India moved atop the Tri-series standings with 10 points from four matches, one clear of Australia. Sri Lanka remains winless from three matches, but picked up two points for the tie.
"It was going both ways. Probably the last ball, the tide was with us," Sri Lanka captain Jayawardene said. "But when you have MS batting, it's always going to be a tough one. One ball, four to get, you back yourself to win the game. But three runs to tie, that's how it goes." Jayawardene said dropped catches and misfielding cost his team "but still, to get two points, I think we can be happy with that." "We were right in it," he said. "We can take positives out of this. We're losing by small margins playing good cricket. If we get that win, momentum might go our way." There was also an element of controversy because India's innings was one ball short. Malinga delivered only five balls in the 30th over, which was missed by on-field umpires and the TV official.
Dhoni said in the past, the third umpire has intervened to ensure such an oversight was rectified.
"Usually that is what has happened to us, it didn't happen in this game — it's fair enough, nothing much can be done now," he said.
After losing Sachin Tendulkar for 15 early, India seemed to be coasting toward victory with Dhoni and opener Gautam Gambhir at the crease until a run out ended their 60-run partnership in the 41st over.
Gambhir was on 91 — following his 92 in the four-wicket win over Australia — when Dhoni pushed to mid-on, called for a single, then changed his mind. Gambhir was stranded and India slipped to 178-5.
Dhoni continued with the tailenders and needed 24 runs off the last two overs. After conceding 15 in the penultimate over, Sri Lanka was relying on Malinga's low-slinging deliveries to contain India.
Malinga held his composure and there were two run outs and one near-miss in the last over before Dhoni faced the final ball. Malinga returned 2-53 from 10 overs and Perera had 2-45.
There were four run-outs in the Indian innings and seven in all for the match.
Earlier, Dinesh Chandimal scored 81 to lead the Sri Lanka innings before he also was run out. He shared vital partnerships with Kumar Sangakkara (31) — 51 for the third wicket — and Jayawardene (43) — 94 for the fourth wicket — after Sri Lanka slumped to 28-2 in the eighth over.
Vinay Kumar took a wicket in the last over of the Sri Lanka innings and returned the best bowling figures of 3-46 for India. Ravichandran Ashwin took 2-30.
India gets a break while Sri Lanka travels to Sydney to play Australia on Friday. India and Australia meet in Brisbane on Sunday.
