Marchisio was sent off in the 59th minute after catching Egidio Arevalo Rios just below the knee with his studs, and the 10-man Azzurri went on to lose the match 1-0 to an 81st-minute Diego Godin header.
The result sees Italy crash out at the group stage for the second successive World Cup, and after the match Prandelli laid the blame for the defeat at the feet of Rodriguez rather than Marchisio.
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"It didn't seem like a red card offense," he told Sky Sport Italia. "There were some tough tackles, but not worthy of a red card. It was a very balanced game, Uruguay never really had a shot on goal despite needing to win. It was a good match tactically and in my view the referee ruined it. He cannot give a red card in that situation, he just can't.
"We got the game with Costa Rica wrong and fought hard with Uruguay against two of the best strikers in the world, though they never caused us problems. It's a great shame that we go out in these circumstances."
Mario Balotelli endured a disappointing afternoon, being booked in the first half before being substituted at halftime, and Prandelli said he made the decision to try and avoid a red card for the striker.
"Balotelli can never understand when he's calm and stressed," the Italy coach added. "He needed to guarantee balance, but I replaced him because I was afraid we'd end up with 10 men."