The unseeded Indian, ranked much lower than Lee (152) at 346, raced to a 6-2 7-5 win over the second seed Korean in the semifinals of the KPIT-MSLTA Challenger in just 63 minutes.
Pranjesh, who is a left-hander, made a nervous start as he began with a double fault but soon got control over the proceedings with Lee also helping his cause by committing a lot of unforced errors.
26-year-old Prajnesh will now fight it out for the title with Frenchman Sadio Doumbia, who knocked out sixth seed Serbian Nikola Milojevic 5-7 6-3 6-2 in the other semifinal.
Prajnesh struck the ball clean and consistently put the ball in the court. He broke Lee in the fifth game after a long rally to take the lead and again broke him in the seventh to cruise to a 5-2 lead.
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He served out the set with an ace in a matter of 24 minutes.
Lee started to play slightly better, engaging the Indian in rallies but Prajnesh was up to the task and broke him in the 11th and served out the match in the next game, again with an ace.
"I had beaten him in Bangkok, so I knew what to expect from him. My gamestyle suited to play him. Being a left-hander I could play on backhand of right-hander high up in his shoulder," Prajnesh, who trains in Germany, said after the match.
The doubles pair of Jeevan Nedunchezhiyan and Vijay Sundar Prashanth were ousted 3-6 6-3 11-13 by France's Hugo Nys and Swiss Luca Margaroli.
Meanwhile, the women's final will be played between Sowjanya Bavisetti and Mihika Yadav.
Left-handed Bavisetti beat sixth seed Pranjala Yadlapalli 6-4 6-1 while Mihika knocked out fourth seed Prarthan Thombare 6-4 5-7 6-1.
The women's doubles trophy was lifted by top seeds Sharmadaa Baluu and Dhruthi Tatachar Venugopal with a 6-4 6-0 win over second seeds Riya Bhatia and Shweta Rana.
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