The General Court of the European Union said there were "internal inconsistencies" in the Commission's 2010 decision.
Of the firms, Air France was fined the largest amount - €182.9m - while KLM was fined €127.2m.
The two carriers merged to form Air France-KLM in 2004.
Other carriers involved were Air Canada, Martinair, British Airways, Cargolux, Cathay Pacific Airways, Japan Airlines, LAN Chile, Qantas, SAS and Singapore Airlines.
Lufthansa escaped a sanction after providing information to the Commission.
The court said that the European Commission had not been clear enough in demonstrating an unambiguous "single and continuous infringement" by the carriers.
Instead, the Commission had found four infringements which it had attributed directly to the carriers on particular routes, the court said.
"Internal inconsistencies" in the decision could infringe the airline's rights of defence, the court added.
Some of the carriers had said that the decision "did not allow them to determine the nature and scope of the infringement or infringements that they were alleged to have committed".

The 31-year-old, from Sheffield, has received the honour for her services to athletics.
Ennis-Hill, who won gold at London 2012 Olympics and silver four years later in Rio, announced her retirement from the sport in October.
At the same ceremony, designer and ex-Spice Girl Victoria Beckham was made an OBE for services to fashion.
More on this story and others in South Yorkshire
Ennis-Hill, who received her honour from the Duke of Cambridge, will receive another World Championships gold medal after Tatyana Chernova was stripped of her 2011 world title for doping.
The 2012 Olympic champion, who was accompanied by her grandparents, mother Alison Powell and husband Andy Hill at the ceremony, said: "Just to hear the national anthem in this kind of moment again is really special.
"I've so many amazing memories of standing on the podium and hearing it and to be here receiving a damehood, which I never imagined I would ever receive, is an incredible honour."
She added: "I've had more than I could ever imagine out of my career so I can't stand here receiving a damehood and wish for any more."
Europe's second-highest court has backed a challenge by 11 airlines against an €800m (£583m) European Commission freight cartel fine.
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Former heptathlete Jessica Ennis-Hill has formally been made a dame during a ceremony at Buckingham Palace.