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The 32-year-old Keralite had been laid low by a bout of the mosquito-borne viral disease ahead of the recent Paris Olympics.
Sen stunned Indonesia's world No. 3 Jonatan Christie in their final Group L match. He will face compatriot Prannoy for a place in the last eight.
Sindhu, vying for a third Olympic medal, took just 29 minutes to dispatch her lower-ranked opponent.
Indian shuttlers Sindhu and Prannoy begin their campiagn on Sunday.
The unseeded Lakshya Sen has third seed and world No. 3 Jonatan Christie of Indonesia in his group.
The Indian contingent features no Kerala woman for the second successive Games.
World No. 10 Prannoy was the last Indian to be eliminated on a day when his compatriot Sameer Verma, mixed doubles pair of Sikki Reddy and B Sumeeth Reddy and Aakarshi Kashyap in women's singles also bowed out.
Aakarshi Kashyap beat Australia's Kai Qi Bernice Teoh to progress to the quarterfinals.
Ashmita Chaliha came from behind to enter the second round of with a hard-fought win over Ester Nurumi Tri Wardoyo of Indonesia.
Indian women's doubles duo of Treesa Jolly and Gayatri Gopichand failed to make the cut.
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