Malaysia's world number one Lee played a full part in an epic contest but was unable to avenge his defeats in the finals at Beijing 2008 and last year's World Championships.
Lin's victory, completed in 79 energy-sapping minutes, made him the first man to retain an Olympic Games Singles title.
Some of the rallies were extraordinary, with both players fully committed in defence and attack.
But that was not the only highlight.
Besides Lin, the rest of the Chinese team showed just how strong they still are by sweeping to gold medals in all five events.
Li Xuerui upset compatriot and world number one Wang Yihan in the women's Singles while Zhao Yunlei won mixed and women's Doubles titles with Zhang Nan and Tian Qing respectively.
Cai Yun and Fu Haifeng won the men's Doubles to complete the set.
The top seeds edged out Denmark's Mathias Boe and Carsten Mogensen 21-16 21-15 at Wembley Arena to ensure China ended the tournament with an emphatic statement that they are set to dominate the sport for some time yet.