The experienced Yoshikatsu Kawaguchi will replace Narazaki, who is suffering from a knee injury he picked up in the 3-2 win over Iceland in Manchester on May 30.
"Kawaguchi will play," Zico told reporters on Tuesday. "It was not really worth taking the risk with Narazaki, even though he is not seriously injured."
Denmark-based Kawaguchi, who last played for Japan in a 1-1 draw against Romania last October, said: "Being left out has been hard for me but it's up to me to show the coach I should be Japan's number one."
Japan, who beat Oman and Singapore in their first two Group Three matches, will be without Europe-based trio Hidetoshi Nakata (groin), Junichi Inamoto (broken fibula) and Naohiro Takahara (lung infection) in Saitama.
India, ranked 139th in the world, last beat Japan in 1970 and Wednesday's game is likely to be an exercise in damage limitation for the visitors.
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