The decision by the Court of Arbitration for Sport (CAS) means Qatar-owned Malaga, who finished sixth in La Liga last season, cannot take up a place in the Europa League next term and eighth-placed Rayo Vallecano or ninth-placed Sevilla will compete instead.
"Shameful, pathetic, unfair that they treat us completely differently to other teams with a lot more [financial] irregularities and debts," Malaga's Spain Under-21 playmaker Isco said on his Twitter feed.
"Yet again they are taking away what we won on the pitch. Neither the players or the fans deserve this."
Rayo, who have not been awarded a licence to compete in Europe by the Spanish football federation (RFEF) due to financial problems of their own, reacted to Malaga's exclusion by saying they would appeal to CAS to try to reverse the RFEF's decision.
Otherwise, Sevilla will compete in Europe's second-tier club competition, a tournament they won in 2006 and 2007 when it was called the UEFA Cup.
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.
European football's governing body welcomed the ruling on its website.
"[Malaga] is therefore excluded from the 2013/14 UEFA Europa League and will be replaced by the next best-placed club in the Spanish domestic league, provided this club has been granted a licence and fulfils all the admission criteria," it added.
"The Spanish football federation (RFEF), within the parameters set by UEFA, confirmed on May 14 that Malaga's application for a UEFA licence had been approved," the club said on their website.
Vicente Casado, the club's director general, said Malaga's finances were in much better shape than some other Spanish clubs and he feared others may fall foul of UEFA rules.
"They wanted a scapegoat, a sacrificial lamb, and they found it, I can't see it any other way," he told local radio.
"We cannot lose our heads in the heat of the moment but it seems this decision was not based in law but was political."
