The Malaysian's final Asian Games ended in heartbreak as he pulled back from a game down against his long-time nemesis but faded in the decider.
Defending champion Lin will face world title-holder Chen Long in the final after his Chinese stablemate easily beat Hong Kong's Wei Nan 21-6 21-10 in the other semi.
But Lee, 31, was left to ponder the ruins of what was undoubtedly one of his last chances to outclass Lin on one of the sport's big stages.
"I have done my best and I accept defeat. Now I'll go back (home) and have a rest before the next tournament."
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Lin said he had been distracted by a disputed line call on one of his returns in the first game, which was called in by the line judge, but ruled out by the umpire.
"There was a misjudgment in the first game and that made me a little bit anxious, but I adjusted well," said Lin, who said he relished any chance to line up against Lee.