The brothers' demotion to the bench is among four changes made by head coach Pablo Lemoine for Saturday's meeting in Bordeaux.
Back-rower Alfonso scored in the 42-12 loss to Japan which was Chile's first ever appearance in a World Cup.
"The first match gave us a lot of information," Lemoine told reporters.
"We have to use the players differently.
"At the end of the second half we suffered a lot from the damage from the changes that came a bit too late, especially in the front row," he added.
Prop Tomas Dussaillant, second-rows Pablo Huete and Santiago Pedrero as well as wingers Jose Ignacio Larenas are the new faces to feature against the Pacific Islanders.
Another pair of brothers, centre Domingo Saavedra and flanker Clemente Saavedra, keep their places with Clemente moving to the back-row from lock.
After Samoa, Chile – the lowest-ranked side in the competition – play former winners England as well as fellow South Americans Argentina in Pool D.
CHILE: Inaki Ayarza; Santiago Videla, Domingo Saavedra, Matias Garafulic, Jose Ignacio Larenas; Rodrigo Fernandez, Marcelo Torrealba; Raimundo Martinez, Clemente Saavedra, Martin Sigren (capt); Santiago Pedrero, Pablo Huete; Matias Dittus, Tomas Dussaillant, Javier Carrasco
REPLACEMENTS: Diego Escobar, Salvador Lues, Esteban Inostroza, Javier Eissmann, Alfonso Escobar, Ignacio Silva, Benjamin Videla, Pablo Casas
COACH: Pablo Lemoine (URU)
