European football's ruling body, which is getting tough on teams that live beyond their means, initially banned Qatar-owned Malaga for two years in December because of overdue payments to rival clubs and Spanish tax authorities.
That was later reduced to a year after the club "regularised its overdue payables" by a March 31 deadline and they appealed to CAS asking for the UEFA decision to be annulled or replaced with less severe sanctions.
However, CAS announced on Tuesday it had rejected the appeal and ruled Malaga, who finished sixth in La Liga last season, would also have to pay the original fine of 300,000 euros.
The Swiss-based court said it would publish the reasons for its decision at an unspecified date.
Malaga reiterated after the CAS decision that they had complied with UEFA rules set out in the organisation's Financial Fair Play (FFP) regulations and deserved to be able to take up their Europa League place.
"The Spanish football federation (RFEF), within the parameters set by UEFA, confirmed on May 14, 2013 that Malaga's application for a UEFA licence had been approved," the club said on their website.
Their Europa League berth will now be taken by Rayo Vallecano, who finished eighth, if the Madrid-based club can resolve their own financial problems.
Otherwise, ninth-placed Sevilla will compete in Europe's second-tier club competition next term, a tournament they won in 2006 and 2007 when it was called the UEFA Cup.
