The Barcelona superstar was initially named in coach Alejandro Sabella's preliminary squad for the final two games of qualification.
However, with their progression already confirmed, the 26-year-old attacker has been released from the squad to recover from his thigh injury.
The Argentine Football Association (AFA) confirmed on its website that Messi, along with Javier Mascherano and Gonzalo Higuain, will not have to meet up with the national team.
Mascherano suffered a hamstring injury at the end of September and has missed Barcelona's last three matches.
Meanwhile, Higuain was not involved in Napoli's Champions League clash with Arsenal due to a calf injury and he also missed their Serie A victory over Livorno on Sunday.
Argentina face Peru on October 11 before travelling to Montevideo four days later to take on Uruguay.