The 13th seeded Indo-French combination went down 6-7, 2-6 to eighth seeds Nikola Mektic of Croatia and Austria's Alexander Peya in an hour and 32 minutes.
In the semi-finals, Mektic and Peya will meet the winners of the last eight clash between Nicolas Jarry of Chile and Maximo Gonzalez of Argentina and the sixth seeded French pair of Pierre-Hugues Herbert and Nicolas Mahut.
This is the second time this year that Bopanna and Roger-Vasselin have come up short at a major tournament. The duo had earlier crashed out of the second round of the Australian Open in January year.
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