Seeded sixth, Paes and Nestor lost lost 4-6 6-7(4) in just 67 minutes to the French-Swiss wild card pair.
Paes has been struggling since making the final of the Delray Beach as this is fourth tournament in a row where he has not moved beyond the second round.
Paes regularly plays with South African Raven Klaasen and for this tournament he paired with Nestor, who parted ways with India's Rohan Bopanna recently.
The sixth seeds saved two breakpoints in the second set which was eventually decided by the tie-break where Paire and Wawrinka prevailed.
