Seventh seeds Paes and Stepanek lost their final Group B contest 6-4 6-7 (5) 8-10 to Spanish pair of Mark Lopez and Marcel Granollers in one hour and 49 minutes.
Paes had qualified for the season finale for the 14th time, having finished runner-up with compatriot Mahesh Bhupathi in 1997, 1999 and 2000 and in 2005 with Serbia's Nenad Zimonjic.
Paes and Stepanek, the US Open winners, have conceded 35 games, the highest in their Group in three matches and even if Alexander Peya and Bruno Soares lose to David Marrero and Fernando Verdasco later in the day, the seventh seeds won't qualify for the semifinals.
Lopez and Granollers have conceded 34 games, one less than Paes and Stepanek, so they are still technically in the race.
Paes and Stepanek end their season together with a 15-8 match record on the season, which includes winning the US Open.
In the match today Lopez and Paes each saved three break point opportunities, including deciding deuce points, in the third and fourth games of the first set.
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