Fifth seeds Paes and Stepanek were tied 5-5 in the first set when their sixth-seeded rivals Marcel Granollers and Marc Lopez of Spain retired due to injury.
The match was halted when Lopez received a lengthy medical timeout due to a calf injury. Two games later, Lopez gestured that he would be unable to continue before limping off the court.
The Indian offered his sympathies to Lopez at the end of the proceedings.
"I wish Marc all the best because both he and Marcel are great guys," said Paes afterwards.
"This is our livelihood and we come out to work hard and put on a show for you guys, so he definitely deserves respect."
The Indian-Czech team grabbed an early break on Lopez's serve to lead 2-1 after Stepanek fired a volley at Granollers.
Even though the Spanish team had fewer opportunities, they made the most of them. A nine deuce game on Lopez's next service outing at 2-4 resulted in six missed break point opportunities for Paes and Stepanek.
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