"The Court refers the case back to the General Court so that it may examine, in the light of the arguments put forward by Intel, whether the rebates at issue are capable of restricting competition", the court said in a statement.
The decision could embolden companies challenging the European Commission, the bloc's antitrust authority, in court over competition decisions-cases the regulator typically wins.
Intel was fined in 2009 when the Commission found that between 2002 and 2007, the company had offered incentives to computer makers Dell, Lenovo, HP and NEC if they bought all of their x86 microprocessors from Intel instead of a rival, AMD.
The commission said Intel foreclosed one of its competitors, Advanced Micro Devices Inc., from the market by granting rebates to four major computer manufacturers on the condition that they purchased all, or nearly all, of their x86 CPUs from Intel.
KitGuru Says: It seems the EU's top court has decided that there wasn't sufficient evidence to prove that Intel's rebates were restricting competition.
An Intel victory could have direct bearing on a similar Commission case involving payments by United States chip maker Qualcomm to computer firm Apple.More news: Hungary and Slovakia must stick or twist — European Union refugee ruling
Last year, Ireland was ordered to claw back €12bn in unpaid taxes from Apple, with the Commission ruling that the company's arrangements in the country amounted to illegal state aid.
Intel also awarded payments to the electronics retail group Media-Saturn in order that the group would sell only those computers containing Intel's x86 CPUs.
This does not mean Intel is off the hook-rather, it means the General Court needs to examine Intel's legal arguments more closely than it did before, potentially giving Intel a chance to have the fine annulled or reduced.
"The commission takes note of today's ruling by the European Court of Justice and will study the judgment carefully", the commission said.
In June the Commission hit Google with a €2.4bn fine over its online shopping services.
But the General Court failed to take those allegations into account when it rejected Intel's appeal in 2014.