Second see Lee Zii Jia, and Denmark's Antonsen registered hard-fought wins on the day.
Two-time Commonwealth Games champion Saina went down 12-21, 21-17, 12-21 to Han Yue of China.
The Indian ace lost 2-1 to Rasmus Gemke of Denmark in Paris.
This was only the second career match between the top two Indian shuttlers.
Lakshya Sen advanaced to the quarterfinals with a 21-9, 21-18 win over compatriot H S Prannoy.
Keralite Treesa and Gayatri registered a 21-15, 21-18 win over world No. 159 Australian pair of Wendy Hsuan-Yu Chen and Gronya Somerville to finish on the podium in their first major event together as a combination.
Sindhu had a comfortable 21-10 21-9 win in her prequarters against Uganda's Husina Kobugabe.
Srikanth lost to lower-ranked Tze Yong Ng in three games to put the defending champions on the backfoot in the final.
Manjunath stunned World Championships silver medallist Kidambi Srikanth 21-17, 15-21, 21-18.
It appeared that the Indians reserved their best for the final where they blanked favourites Indonesia 3-0 to lift the Thomas Cup in style.