The Irish government welcomed the ruling, saying "there was no special treatment provided" to the US company.
But the iPhone maker's court victory yesterday, toppling the decision, risks leaving her crusade against unfair tax deals in tatters.
"According to the General Court, the Commission was wrong to declare that [Apple Sales International] and [Apple Operations Europe] had been granted a selective economic advantage and, by extension, State aid", the court wrote in a statement.
The Commission also claimed that Ireland had allowed Apple to attribute almost all of its Eu earnings to its head office in the country, despite existing only on paper and effectively avoiding taxes across other member states.
Because the EU Commission had argued that the absence of staff and tangible assets outside of Ireland indicated that the IP must have been assets of the branches, they failed to consider what Irish tax may have been due had normal transfer pricing rules been followed to calculate the taxable profits of those branches excluding the IP.
The decision effectively canceled an August 2016 European Commission decision.
Apple contested the decision that obligated the company to return such an amount to the Irish State, in a court case that dragged on in Luxembourg, and has now been supported by the EU General Court. "We're proud to be the largest taxpayer in the world".
The European Commission on Wednesday unveiled plans to clamp down on aggressive corporate tax planning regimes that distort the level playing field of the EU's single market, a move it said would aid Europe's recovery from the coronavirus pandemic. Her method is to deploy European Union state-aid laws to go after secretive preferential agreements that big businesses often reach with tax authorities. Based on the Starbucks ruling and today's Apple ruling, it would appear that the European Union courts don't necessarily disagree with Vestager's crusade against multinational tax dodgers - but it does care about the Commission doing its homework to prove its case. If Member States give certain multinational companies tax advantages not available to their rivals, this harms fair competition in the EU.
Her job policing subsidies "needs to go hand in hand with a change in corporate philosophies and the right legislation to address loopholes and ensure transparency", she said.
The case is likely to be appealed by the EU, limited to points of law, and brought before the European Court of Justice within two months and ten days of today. Google and Amazon have other court appeals pending as they seek to overturn decisions that they broke European competition laws.
The ruling is likely to be taken into account in pending cases against Ikea, Nike, and other worldwide firms.
'Brussels will no doubt appeal. European countries and the USA are at an impasse in worldwide talks on the topic, with Europeans pushing for rules that would make tech companies pay more levies where their customers are based, and Americans rejecting a system that doesn't apply to all companies.
As a result of this, France, Spain, Italy and Austria made clear their intentions to push forward with a digital services tax, following the failure to agree on bloc-wide measures. The decision can be appealed.