The current world number one from Malaysia dropped to his haunches at 16-19 down and tried to recover but had to retire from the match at 20-17 — leaving Lin, who is world and Olympic champion, to take the title 16-21, 21-13, 20-17.
Lee had been hoping to end a run of high-profile defeats at the hands of Lin — widely regarded as the game’s best-ever player — who beat him in the previous world title men’s singles final and in the two last Olympic finals.
Lin, 29, known as “Super Dan”, was making his comeback at the tournament with a controversial wildcard place after a year on the sidelines to spend time with his family.
The two badminton legends put on a brilliant display in the first set in front of a packed Tianhe gymnasium in the southern Chinese city of Guangzhou.
Lin took an early lead, leaving the crowd gasping with an almost involuntary lightning reflex return at the net to go 5-3 up. The return was so quick that he hardly seemed to know about it himself.
Lee got back on level terms but Lin got the better of a titanic rally to go into the break 11-10 up.
The two stayed neck and neck, showing off their best badminton — a nimble Lee leaping around the court and Lin moving fluidly often at full stretch to reach the Malaysian’s well-placed shots.
Lee pulled ahead with Lin berating himself after putting a return long to go behind 14-18, and the Malaysian capitalised to take the first game 21-16.
Lin came out fighting in the second, romping to a merciless 11-1 lead with Lee leaving shots to go long that dropped just in.
As the temperature soared in the stadium with the air conditioning seemingly off during the second game, the crowd fanned themselves furiously and Lee battled to catch up, but Lin took the second 21-13.
Lee came out fighting in the third game with the temperature in the stadium still roasting hot. Lin winced as he hit the net again to drop 4-8 behind.
But the defending champion battled back, with precision shots to the baseline sailing past Lee to go into the break 11-10 up.
The battle ended after Lin went 19-16 up in the third with a smash down the line and Lee crouched down on his haunches.
Lee’s legs were sprayed by a doctor called onto the court, and he won the next point with lightning returns before dropping to the floor again in the middle of the next point.
The crowd shouted his name in encouragement and Lin went over to his opponent’s side of the court to speak to him. But the umpire announced the Malaysian was retiring injured at 20-17, leaving a shirtless Lin to celebrate while Lee was stretchered off.