Venezuela dominated on their home turf but struggled to break through eliminated Paraguay's sturdy defence, leaving them sixth with 20 points in the South American group and outside the qualifying places.
The top four in the group go through to the 2014 finals in Brazil with the fifth-placed team qualifying for a playoff against Jordan.
Paraguay's Edgar Benitez opened the score in the 28th minute before substitute Luis Manuel Seijas managed to secure a draw for Venezuela minutes before the final whistle.
"There's a bitter aftertaste when one tries to achieve something and it slips away by very little," Venezuela's coach Cesar Farias said.
Colombia qualified on Friday with a 3-3 draw with Chile to join group leaders Argentina, who secured their ticket last month, in Brazil next year.
Ecuador (25), Chile (25) and Uruguay (22) are still in contention for the finals with one match remaining in the marathon qualification campaign.
(Reporting by Diego Ore in Caracas; Writing by Alexandra Ulmer; Editing by Greg Stutchbury)
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