Juventus defender Caceres will not recover in time from an ankle injury and will miss the tournament that begins in Chile on June 11.
Attacking midfielder Gaston Ramirez was also left out of the 27-man squad that will be cut back to 23 on the eve of the tournament.
Holders Chile join group winners Argentina in Copa America Centenario knock-out stage
Uruguay will also be without Luis Suarez while full back Jorge Fucile, the only home-based player in the squad, was a surprise inclusion.
Uruguay, who have won the Copa America more than any other nation, are in Group B and will face Jamaica, Argentina and Paraguay.
They play a final friendly against Guatemala in Montevideo on June 6.
Goalkeepers: Fernando Muslera (Galatasaray), Martin Silva (Vasco da Gama), Rodrigo Munoz (Libertad)
Defenders: Maximiliano Pereira (Benfica), Matias Aguirregaray (Estudiantes LP), Jose Maria Gimenez (Atletico Madrid), Diego Godin (Atletico Madrid), Sebastian Coates (Sunderland), Emiliano Velazquez (Getafe), Gaston Silva (Torino), Alvaro Pereira (Estudiantes LP)
Midfielders: Mathias Corujo (U. de Chile), Jorge Fucile (Nacional), Camilo Mayada (River Plate), Alvaro Gonzalez (Torino), Carlos Sanchez (River Plate), Egidio Arevalo Rios (Tigres), Walter Gargano (Nápoli), Guzman Pereira (U. de Chile), Nicolas Lodeiro (Boca Juniors), Cristian Rodriguez (No Club), Giorgian De Arrascaeta (Cruzeiro)
Forwards: Diego Rolan (Bordeaux), Jonathan Rodriguez (Benfica), Edinson Cavani (PSG), Cristhian Stuani (Espanyol), Abel Hernandez (Hull City)
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