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Bopanna and his partner Matthew Ebden of Australia beat the top-ranked pair of Dutchman Wesley Koolhof and Briton Neal Skupski 6-3, 2-6, 10-8 to claim their second title together and first of the season.
India lost the tie 2-3 on Saturday with Holger Rune starring for Denmark.
Unseeded Bopanna and Sania lost 6-7(2) 2-6 to Brazilian pair of Luisa Stefani and Rafael Mataos in the final at Rod Laver Arena.
The unseeded Indian pair knocked out third seeds Desirae Krawczyk and Neal Skupski 7-6(5), 6-7(5), 10-6 in the semifinal that lasted one hour and 52 minutes.
The Indians progressed after Jelena Ostapenko and David Vega Hernandez pulled out of the mixed doubled quarterfinals.
The Indian pair defeated Japan's Makoto Ninomiya and Uruguay's Ariel Behar 6-4, 7-6(11-9).
N Sriram Balaji and Jeevan Nedunchezhiyan's were also halted by the French duo of Jeremy Chardy and Fabrice Martin in the second round of the men's doubles.
Sriram Balaji and Jeevan Nedunchezhiyan stunned fifth seeds Ivan Dodig and Austin Krajicek in the opening round.
The veteran doubles ace has opted out of the away tie due to a knee injury.
They went down fighting to Jean-Julien Rojer and Marcelo Arevalo 6-4, 3-6, 6-7.