Murofushi's own reputation was not tarnished by the ban, the CAS said in an explanation of its decision to reject the athlete's appeal against the ban.
The 2012 Games bronze medallist and the JOC had appealed to the CAS after the IOC barred him from the commission for violating election rules.
"The panel concludes to uphold the decision of the (IOC)Executive Board and in turn dismisses the appeal," the CAS said.
"Having said this the panel would like to add that - at least to a significant extent - the candidate was a victim of an overzealous (national Olympic Committee) and that his own actions were neither motivated by a desire to cheat nor can they be equated to dishonesty.
"His reputation and integrity as a sportsman, therefore, remain completely untarnished."
The 38-year-old Murofushi had collected enough votes to secure a seat on the commission in the election during the London Games, but the IOC declared the result void, saying he had violated campaign rules.
Taiwanese Athens 2004 Games taekwondo gold medallist Chu Mu-yen was excluded for similar reasons and his CAS appeal was rejected in March.