The seventh seeded Indo-Czech pair fought hard before losing 4-6 6-7 (5) to their Spanish rivals in one hour and 29 minutes.
Now Paes and Stepanek, the US Open winners, must beat Marcel Granollers and Mark Lopez for making it to the next stage without any favour from other teams.
The Indo-Czech pair had beaten Alexander Peya and Bruno Soares on Tuesday.
The top two teams in each group will qualify for the semifinals.
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In the match today, Marrero and Verdasco mixed up net and baseline play to negotiate a break of the Stepanek serve to 30 for a 5-4 lead in the first set. Verdasco clinched the 34-minute opener with a hold to love, finishing with an ace. The pair had lost just two of their service points.
Paes lost his serve to 30 in the opening game of the second set, but the Indian-Czech team recovered from 0-2 by winning three straight games. Both teams completed routine service holds through to the tie-break.
The Spaniards won 34 of their 41 first service points in total.