On remand, the General Court must consider Intel's argument about whether the rebates were capable of restricting competition.
The lower tribunal - the EU General Court - has to examine "whether the rebates at issue were capable of restricting competition".
The Commission and Intel said on Wednesday's they were analysing the verdict and that it was too early to comment.
The decade-long case could drag on for several more years as Intel could appeal the General Court's judgment following the re-examination, if it goes against the company.More news: Parliamentarians demand withdrawal of presidential medal given to Suu Kyi
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Historically, European courts have effectively rubber-stamped European Commission antitrust decisions and fines. That ruling was seen then as a rebuke to Intel and a sign to the community that no company is above the rulings of the court.
Because of its ruling that exclusivity rebates were automatic infringements of Article 102 TFEU the GC did not consider all of Intel's arguments regarding the Commission's alternative analysis of the effects of the rebates on competition.
Nevertheless it will be a big encouragement to other large USA tech companies that have fallen foul of the EU's Competition Authority, Qualcomm is being investigated over payments made to Apple over the use of its chips in iPhones and iPads and Google is also being investigated over its contract terms with phonemakers and networks using its Android software. The European Commission, the European Union's executive arm, found in 2009 that the company had offered rebates and incentives to computer makers to favour its products over those of rival AMD. "The ECJ's decision is also good news for consumers, because dominant companies may now have more flexibility in offering rebates to high-volume buyers". The EU also said Intel made payments to electronics retailer Media Saturn Holding on the condition that it only sold computers containing Intel's microprocessors. "The case should be referred back to the General Court for a fresh review".
In June, the European Commission hit Google with a record fine of €2.4 billion ($2.7 billion) for violating antitrust regulations.
Regulators have generally frowned upon rebates, especially those offered by dominant companies, on the theory they are anti-competitive in nature.