The 34-year-old from Chinese Taipei tapped in a 1-foot birdie putt on the second extra hole to knock off Northern Ireland's Rory McIlroy for the victory.
Francesco Molinari of Italy was ousted on the first playoff hole.
Lin, already a winner on the Asian Tour, shot a 3-under 67 in the final round to tie McIlroy and Molinari at 15-under-par 265 and force the three-way playoff.
He endured a missed birdie putt at the 18th hole in regulation that would have given him the win outright, then an errant drive on the first extra hole that looked like it would knock him out of the playoff.
Lin recovered, however, with a spectacular approach shot to 6 feet ' he took a mighty whack from behind a tree ' to set up a birdie putt that was interrupted momentarily by a shouting fan.
McIlroy, who closed with a 5-under 65 in the final round, matched Lin's birdie effort on the first extra hole with an approach to 3 feet from the middle of the fairway.
Molinari, after also making it into the playoff with a 65, found the rough off the tee and missed a 15-foot birdie putt to get knocked from the extra session.
Back at No. 18 for the third straight time, it was McIlroy's turn to send his drive into the trees on the left side of the fairway, while Lin split the middle with his.
But ' like Lin had done moments earlier ' McIlroy took his own mighty hack from behind a tree, sending a swinging hook shot to the back of the green to preserve a birdie opportunity.
The great shot mattered little.
Lin stepped to his ball at the bottom of the fairway and calmly sent a wedge shot towards the hole. It stopped just a foot from the cup, and Lin threw his right fist in the air.
When McIlroy missed his long birdie effort on the left side of the hole, all Lin needed to do was tap in his short putt for the win.
'This is my first European Tour win and my feelings cannot be described,' Lin said through an interpreter. 'With this win I can reassure myself that what I am doing is right.'
The three-way playoff ended a tight final round at Hong Kong Golf Club that also saw third-round leader Oliver Wilson and Hall of Famer Bernhard Langer, among others, jockey for the win.
Meanwhile, Wilson (71) made three consecutive bogeys late in the round to fall into a five-way tie for sixth place at 12-under 268 ' despite sharing the lead with four holes left.
Langer (69) went bogey-birdie-bogey on his last three holes to join Wilson, David Gleeson (66), Iain Steel (66) and Richard Sterne (66) in a share of sixth.
The round ended as it should have, the playoff seeming all but inevitable as the final round wore on and no clear favorite emerged.
Lin, for his part, joined a four-way tie for the lead with a 25-foot birdie putt on the 12th hole. He preserved his share of that lead with another birdie at the 13th, but missed a 6-foot birdie putt at the 18th with a chance to win in regulation.
McIlroy, the 19-year-old rising star who is still seeking his first win, drained a 20-foot birdie putt at the 15th hole that gave him a share of the lead. But it was his only birdie in the final nine holes of regulation.
'It was not meant to be, but it still has been a great week for me,' said McIlroy. 'I couldn't have done much more.'
Molinari eagled the 13th and birdied the 14th to soar up the leaderboard and take the lead by himself, but he bogeyed the 15th. Another birdie at the 17th kept him in it, and he was the first player in the clubhouse at 15 under after coming within inches of a closing birdie at the 18th.
'I think that the pity is just the putt on the 72nd hole that went really, really close to going in,' said Molinari, 'but it's all right.'
Colin Montgomerie and John Daly also had good showings at the second event on the European Tour's 2009 schedule.
Monty closed with a 69 and tied for 15th place at 10-under 270, while Daly scorched the course for a 62 on Sunday that earned him a share of 17th at 9 under.
The last time Daly came close to a number that low was his 63 in the second round of the 2007 Frys.com Open.