CAS general secretary Matthieu Reeb told reporters that the Premier League champion’s appeal, made in June, had been judged inadmissible, Reuters reported.
UEFA had opened an investigation into City over potential breaches of its break-even rule in March after German publication Der Spiegel reported the club’s Abu Dhabi owners inflated sponsorship agreements to comply with requirements.
In May, UEFA investigators referred the case to the Club Financial Control board’s judicial body for possible sanctions.
City appealed in June against that decision, saying at the time that UEFA investigators had ignored “a comprehensive body of irrefutable evidence provided by Manchester City.”
The club has said that the accusation of financial irregularities “remains entirely false” and it is confident of a positive outcome.
Financial Fair Play rules are intended to prevent clubs receiving unlimited amounts of money through rich owners and inflated sponsorship deals.
Clubs who have breached the rules can ultimately be barred from European competition, but negotiated settlements are more common.
Seven-time European champion AC Milan became the biggest club to be banned when it was barred from this season’s Europa League for overspending.
Reeb said the City appeal had been thrown out because the UEFA case had not run its course.
“The UEFA decision was not final, there is still another stage before and a possible final decision to be rendered,” he said.
He added that City could appeal again once UEFA had made its final decision.
Separately, City was fined 370,000 Swiss Francs (£290,052) by global soccer body FIFA in August for breaches of rules regarding the transfer of under-18 players.
However, the club avoided a transfer ban — a common sanction in such cases — after FIFA said it had “accepted its responsibility.”