The top-seeded Indo-Canadian pair lost 6-3 5-7 8-10 to the unseeded rivals in one hour and 21 minutes.
Paes had combined with Nestor to win his first title of the season at Winston-Salem (USA) in August.
After that Paes had won US Open with regular partner Radek Stepanek.
Meanwhile, Somdev Devvarman won his first round in the Shanghai Masters Qualifiers as he edged past local wild card
He now needs to beat Japanese Tatsuma Ito to make the main draw. It will be third meeting between Somdev and Tatsuma, whom the Indian beaten in 2009 in Washington and at at Atlanta in 2011.
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