Luis Suarez had put the home side ahead four minutes earlier with a fine goal that looked to have breathed new life into 2010 semi-finalists Uruguay's campaign to reach Brazil 2014.
Benitez took advantage of a mistake in central defence by Uruguay captain Diego Lugano to latch onto the loose ball and shoot past Fernando Muslera in the 86th minute.
Suarez shot low inside the far corner from midfielder Nicolas Lodeiro's cross in the 82nd minute as Uruguay looked to end a run of four matches without a victory.
Uruguay have 13 points from 10 matches with Paraguay, quarter-finalists in 2010, still rooted to the bottom of the nine-nation South American group with eight.
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