Diego Godin's 81st-minute header settled a tense encounter, which also saw Italy midfielder Claudio Marchisio dismissed, to send the South Americans through and dump the Azzurri out.
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"The game was decided by the referee," the 29-year-old told Sky Italia.
"It's a shame because we deserved it [to go through]. During the first half there had been many situations with different treatments - the expulsion of Marchisio was ridiculous and that, along with the lack of punishment for Suarez has changed everything.
"Eventually it proved decisive. Suarez is smart because Fifa allow it because they want to their champions to play. The referee saw everything, but did not have the courage.
"There are episodes that affect the game. The action is clear, they say that the referees are informed on the players, but obviously they are not."