The 14th seed Indo-French pair shocked the third seed Austrian-Brazilian combination 6-4 4-6 6-7 (5) 6-2 in two hours and 17 minutes.
They will now fight it out with sixth seeds Robert Lindstedt of Sweden and Daniel Nestor of Canada for a place in the semifinals.
Bopanna and his partner saved five of the six break chances they faced while converted three of 12.
The Indian and his new partner fired 18 aces to to six of their rivals.
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Mahesh Bhupathi and his partner Julian Knowle are also featuring in today's pre-quarterfinals. The eight seeded Indo-Austrian pair is clashing with Canadians Jesse Levine and Vasek Pospisil.
Fourth seeds Leander Paes and Radek Stepanek face 15th seed Polish pair of Lukasz Kubot and Marcin Matkowski.
Sania Mirza will also play two matches today. In the women's doubles she and Liezel Huber lock horns with Shuko Aoyama of Japan and Chanelle Scheepers of South Africa.