The 31-year-old has been an integral part of the Spain team who won Euros 2008 and 2012, and the World Cup in 2010, but he has been struggling with a groin problem for the last few weeks of the La Liga season.
The other two players to drop out of the provisional list from last Monday were Manchester City's versatile midfielder Javi Garcia and Real Betis midfielder Benat Etxebarria, the country's federation said in a statement.
The 23 players called up will gather at Los Rozas just outside Madrid on Tuesday, apart from Barcelona's Gerard Pique who has been given permission to join the group in Miami due to family reasons.
The world and European champions have two friendlies in the United States before heading to Brazil, against Haiti in Miami on June 8 and Ireland in New York three days later.
For the Confederations Cup, Spain have been drawn in Group B with Uruguay, Tahiti and Nigeria and they open the tournament in Recife on June 16 against the 2011 Copa America winners.
The eight-nation warm up event for next year's World Cup runs from June 15 to 30.
Goalkeepers: Iker Casillas (Real Madrid), Victor Valdes (Barcelona), Pepe Reina (Liverpool)
Defenders: Alvaro Arbeloa (Real Madrid), Sergio Ramos (Real Madrid), Gerard Pique (Barcelona), Cesar Azpilicueta (Chelsea), Jordi Alba (Barcelona), Ignacio Monreal (Arsenal), Raul Albiol (Real Madrid)
Midfielders: Javi Martinez (Bayern Munich), Xavi (Barcelona), Andres Iniesta (Barcelona), Sergio Busquets (Barcelona), Santi Cazorla (Arsenal)
Forwards: Cesc Fabregas (Barcelona), David Villa (Barcelona), David Silva (Manchester City), Roberto Soldado (Valencia), Pedro (Barcelona), Juan Mata (Chelsea), Jesus Navas (Sevilla), Fernando Torres (Chelsea).