In his first selection since last month's European Championship triumph, Del Bosque also omitted Juan Mata, Jordi Alba and Javi Martinez, who took part in Spain's failed bid for a medal at the London Olympics after competing at Euro 2012 with the senior squad.
"In the case of Xavi, I spoke to him yesterday and we decided not to bring him so that he can prepare well," Del Bosque told a news conference at the Spanish football federation (RFEF) headquarters near Madrid.
"However we can help so that things work better, above all in the case of players who are more important than us, we will help," he added of Barcelona playmaker Xavi, 32, who suffered from a niggling calf injury last season.
Spain begin their qualification campaign for the 2014 World Cup in Brazil away to Georgia on September 11 and are in a Group I which also features France, Belarus and Finland.
Squad for Puerto Rico friendly:
Goalkeepers: Iker Casillas (Real Madrid), Pepe Reina (Liverpool), Victor Valdes (Barcelona).
Defenders: Alvaro Arbeloa (Real Madrid), Sergio Ramos (Real Madrid), Raul Albiol (Real Madrid), Gerard Pique (Barcelona), Ignacio Monreal (Malaga), Juanfran (Atletico Madrid).
Midfielders: Xabi Alonso (Real Madrid), Sergio Busquets (Barcelona), Santi Cazorla (Arsenal), Cesc Fabregas (Barcelona) Andres Iniesta (Barcelona).
Forwards: David Silva (Manchester City), Jesus Navas (Sevilla), Pedro (Barcelona), Fernando Llorente (Athletic Bilbao), Fernando Torres (Chelsea).
