The 27-year-old overcame her Korean rival 11-6, 11-9, 4-11, 5-11, 11-7 in 41 minutes to set up a last-four clash with World No. 24 Zhang Rui of China.
Manika started on a rosy note against Choi, winning the first two games but lost the next two before lifting her game by a few notches to win the fifth and deciding game and seal a last-four spot.
Earlier, Zhang defeated Yi Chen of China 3-2 to make it to the semifinals.
The other semifinal will be an all-China affair with World No. 18 Siqi Fan taking on World No. 30 Lui Weishan.
Siqi got the better of Cheng I-Ching 3-1 (14-12, 9-11, 11-6, 11-9), while Lui overcame Tianyi Qian 3-0 (11-9, 11-7, 11-6).
On Thursday night, mixed-doubles top seeds Manika and Sathiyan Gnanasekaran bowed out of the title contention after losing 1-3 to the Korean duo of Lim Jonghoon and Shin Yubin in the semifinal.
In the other semifinal, Chinese pair of Kuai Man and Lin Shidong defeated Wong Chun Ting and Doo Hoi Kem of Hong Kong.
The mixed-doubles final will take place on Friday night along with the men's doubles and women's doubles finals.
In the other semifinal, Chinese pair of Kuai Man and Lin Shidong defeated Wong Chun Ting and Doo Hoi Kem of Hong Kong.
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