Singh drove to the front of the green at the third playoff hole, the 360-yard, par-four 17th at Saujana Golf and Country Club.
Harrington's tee shot was short of the green and he chipped up to within seven feet of the hole. Singh lagged his putt to two feet and tapped in for birdie, which became the difference when Harrington missed with his bid to extend the playoff.
There was a chance Singh wouldn't have needed extra holes had he kept his ball in bounds off the tee at 17 in regulation. The reigning Masters champ was penalized for his wayward drive and ended up with a double-bogey six to drop back to 13-under par.
Meanwhile, Harrington was birdying the 16th -- his third birdie in the span of four holes -- to make up for a slow start to his final round. The Irishman took a two-shot lead at 15-under headed into the last two holes.
But Singh, playing one hole ahead of the leader, pitched to a foot to set up a birdie at the par-five 18th. Harrington knocked his approach at 17 over the green and was unable to get up and down to save par. When Harrington parred the last to complete his round of two-under 70, he and Singh stood tied at 14-under-par 274.
'I thought I had given it away with the double-bogey on the 17th,' said Singh, who shot a four-under 68 on Sunday. 'But then I made birdie. I'm glad the way things turned out. Padraig played very well all round and came back strongly at the end.'
Singh, who won his first international title at the 1984 Malaysian PGA Championship, collected the $151,660 winner's share for his eighth victory on the European Tour.
Extra holes began at the 18th, where Singh found a fairway bunker off the tee. He knocked his second shot down the fairway then hit his approach to 12 feet. Harrington, meanwhile, laid up short of the green and pitched his third shot to 25 feet. After Harrington's birdie putt narrowly missed the cup, Singh's attempt at the win lipped out and the two players putted out for pars and went back to the tee at 18.
Singh applied the pressure the second time around with a third shot that nearly hit the hole, then spun back to about 10 feet. But Harrington put his approach just inside Singh's, and the duo traded birdies by holing their putts then moved on to the 17th.
Singh posted five birdies over a nine-hole span from the eighth to the 16th to climb to the top of a jammed leaderboard. The native of Fuji began the final round two back of Harrington, who matched Singh's score of 68 in the weather-suspended third round that was completed earlier on Sunday.
Harrington, the runner-up here last year as well, was fine with his finish, all things considered.
'I'm delighted to have finished second considering I'm working on my swing,' he said. 'If I had been offered second place coming out here I would have been thrilled, not knowing what my form was.'
American Ahmad Dan Bateman and Charlie Wi of Korea, who each had a share of the lead during the final round, tied for second at 12- under. Bateman carded 67 on Sunday while Wi closed with a 69.
Denmark's Soren Hansen finished alone in fifth at 10-under par, one stroke better than Ter-Chang Wang of Taiwan.
New Zealand's Michael Campbell, the winner of the Heineken Classic two weeks ago, offset four birdies with five bogeys for a final-round 73 and a share of seventh place at minus-eight.
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