The Palmeiras playmaker sat out the clash in Santiago, which saw Jorge Sampaoli's side come from two goals down to seal victory.
Valdivia has 55 caps to his name and could be crucial to Chile's efforts in Brazil after contributing eight assists in 13 qualifying appearances.
Though conspicuous by his absence in Saturday's win, the 30-year-old is confident of making Sampaoli's 23-man final squad, with Chile facing Australia, Spain and Netherlands in Group B
"I had some discomfort in the calf area and in conjunction with the medical staff, we decided that it was best not to play," he told La Tercera.
"I don't have any injury, I'm quietly waiting to be in the squad."
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