Fifth seed Saina lost 8-21 12-21 to top seed and world number one Yihan Wang in a women's singles match that lasted for 33 minutes at the Xincheng Gymnasium.
Jwala and Diju, however, held their nerves in crucial moments to register a 17-21 21-19 21-9 win over Robert Blair of Scotland and Briton''s Gabrielle White in a 46-minute match.
The world number 56 pair will take on the Korean duo of Yeon Seong Yoo and Ye Na Jang in the semifinals on Sep 17.
The 21-year-old Saina was no match for the Chinese as she sent down as many as 23 smash winners against eight by the Indian. She also played better at the nets, registering 13 winners compared to Saina's four.
Yihan did not give Saina a chance as she opened up a 2-0 lead before moving in gaint strides to pocket the first game.
The second game was no different as Yihan reeled off eight straight points from 4-3 to create a huge gap which Saina could never bridge.
Saina had lost in the quarterfinals of the World Championship as well last month.
While Saina had an off day, Jwala and Diju fought back from a game down to win in mixed doubles.
The Indian duo took time to get into the groove and after lagging 5-13, they narrowed the gap to 17-19 before allowing their rivals to walk away with the first game.
However, Jwala and Diju bounced back in the second game with the help of some deft net play and coordination as they opened up a 13-8 lead, which they held on to draw level.
In the decider, the Indian pair dug into their vast experience and broke off from 3-all as Blair and White faltered.