Gago, who helped engineer Friday's victory, was released by coach Alejandro Sabella on Sunday, joining injured striker Sergio Aguero and suspended top scorer Gonzalo Higuain on the sidelines.
Argentina face Bolivia at high altitude in La Paz, where former coach Diego Maradona's team were crushed 6-1 in a qualifier four years ago.
"The altitude is an abnormal factor we're not accustomed to. You have to adjust your mind to it," said midfielder Leonardo Ponzio, who played in Argentina's last qualifying victory in La Paz in 2005.
"We must make the most of the greater skills of our forwards... who impose a different rhythm to what you see normally," Ponzio told the state news agency Telam.
Sabella is keeping his cards close to his chest for the daunting trip to the Hernando Siles 4,000 metres above sea level where he is expected to play five men across midfield.
His team lead the nine-nation South American group, four points ahead of Colombia and six in front of Ecuador. Bolivia are one from bottom 15 points behind Argentina.
The top four teams at the end of the qualifiers in October will go through to the Brazil finals. The fifth-placed team, at present Venezuela, will enter a play-off against an Asian qualifier for another berth.
