The Real Madrid playmaker was in line to collect his second international cap in the match in Geneva, but the national team have confirmed he has returned to the Spanish capital "as a precaution" following tests on his left ankle.
Isco was an unused substitute in his country's 2-0 victory over Finland in FIFA World Cup qualifying on Friday, and it is now clear that he was deemed unfit to take part prior to the trip to Helsinki.
However, despite the 21-year-old's absence, manager Vicente del Bosque has opted against calling up a replacement for the match against Chile.
"Francisco Roman Alarcon 'Isco' leaves the Spanish national team training camp as a precaution," a statement from the Spanish Football Federation read.
"The discomfort is in his left ankle, although tests have ruled out any anatomic evidence of injury.
"The player was tested last Wednesday, and we have been advised to use caution.
"The complete medical report with radiological tests performed will be sent to the medical services of Real Madrid, with whom the doctors of the team have maintained continuous communication.
"National coach Vicente del Bosque has decided not to call any player instead."
Isco moved to the Santiago Bernabeu from Malaga in the close-season and has made an immediate impact for his new side, scoring three goals in their first three La Liga games.
