Paes and his German partner Andre Begemann lost a close first round encounter against French-Israeli pair of Stephane Robert and Dudi Sela in just under two hours by 6-2 5-7 4-6 margin.
Bopanna, who is partnering Frederik Nielsen of Denmark were blown away by American Brian Baker and Kiwi Marcus Daniell 2-6 6-7 (5-7).
However there was some cheer for the Indian fans as Sania and Dodig, who have won the US Open mixed doubles title in 2014 made a fluent start to their campaign with a 6-4 6-4 straight set win over US pair of Donald Young and Taylor Townsend in just 62 minutes.
In the junior girls' event, India's Pranjala Yadlapalli beat American Victoria Emma 6-3 6-2.
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Bopanna, who hasn't had a great run in the Grand Slams of late as the Indo-Danish pair were broken twice before they conceded the first set 6-2.
It was turning out to be a cakewalk for the Kiwi-US pair as they were ready to serve for the match at 5-3 before Bopanna-Nielsen broke back to make it 5-5 raising visions of a fightback.
Paes and Begemann started their encounter in a resounding manner with two service breaks in the first and fifth game, grabbing the first set at 6-2.
Enjoying a service break in the second set as well, the Indo-German pair looked like serving out at 5-4 before Sela and Roberts got a break back in the 10th game while getting another break in the 12th game to win the set 7-5.