The mercurial midfielder was sidelined after pulling a muscle in his right leg while training with his club Al Ain in the United Arab Emirates, Chilean media said.
Striker Hector Mancilla, who has been in prolific form for Mexican champions Toluca, was included, one of six strikers named in the 22-man squad by former Argentina coach Marcelo Bielsa.
Mancilla was topscorer in the Mexican Apertura championship which Toluca won in December and has already notched eight goals in 11 games in the Clausura which is played in the second half of the Mexican season.
Bielsa continued to overlook Inter Milan striker Luis Jimenez and decided not to recall volatile defender Gary Medel, who on Sunday played his first match for Universidad Catolica since suffering a car crash at the start of the year.
Chile, who beat Argentina 1-0 in their last qualifier in October, visit neighbours and bitter rivals Peru on Sunday and host Uruguay three days later.
Chile are fourth in the 10-team South American group with 16 points from 10 games. The top four teams qualify for South Africa and the fifth plays off against the fourth side from CONCACAF.
Goalkeepers: Claudio Bravo (Real Sociedad), Miguel Pinto (Universidad de Chile), Christopher Toselli (Universidad Catolica)
Defenders: Arturo Vidal (Bayer Leverkusen), Mauricio Isla, (Udinese), Ismael Fuentes (Chiapas), Pablo Contreras (PAOK Salonika), Waldo Ponce (Velez Sarsfield), Rodrigo Tello (Besiktas), Roberto Cereceda (Colo Colo), Gonzalo Jara (Colo Colo)
Midfielders: Marco Estrada (Universidad de Chile), Manuel Iturra (Universidad de Chile), Carlos Carmona (Reggina), Pedro Morales (Dynamo Zagreb), Matias Fernandez (Villarreal)
Forwards: Alexis Sanchez (Udinese), Fabian Orellana (Audax Italiano), Humberto Suazo (Monterrey), Mark Gonzalez (Real Betis), Jean Beausejour (America-Mexico), Hector Mancilla (Toluca)
