World Championships bronze medallist Lakshya had advanced to the semis after his opponent Lu Guang Zu of China gave a walkover.
Lee saved one match point before Lakshya sealed the win.
He became the youngest Indian male shuttler to win a World Championships medal.
Highlights, All England Open 2022, Lakshya Sen vs Lee Zii Jia Semi-Final As it Happened: Lakshya Sen Beats Lee Zii Jia in the Final Round to book a berth in the Final of the All England Open 2022.
Final round coming up Lakshya Sen won the first round by 21-13 and lost the second round 21-12.
Padukone 1980 and Gopichand 2001 are the only two Indians to have won the prestigious tournament.