Fifth seed Prannoy, who had beaten Yuqi at the Badminton Asia Team Championships last year, failed to produce his best game and went down 19-21 11-21 to the second seeded Chinese, who had reached the finals at All England last week.
Earlier, fourth seeded Indian mixed doubles pair of Pranaav Jerry Chopra and N Sikki Reddy also had suffered a 19-21 17-21 loss to fifth seeded Chinese duo of Zhang Nan and Li Yinhui.
In the second game, Yuqi was more dominant as he broke off at 7-7 to distance himself from the Indian and eventually seal his place in the semifinals without much ado.