The EU's general court has handed tech giant Apple a win by overruling the European Commission's decision to make the U.S. iPhone maker pay backdated taxes. 

In 2016 the Commission ruled that Ireland must seek 14.3 billion euros ($16.4 billion) from Apple for the period between 2003 and 2014. It said the taxes had not been paid because the rules were changed in a way that effectively granted Apple government financial help. 

The ruling from the bloc's second-highest court is a major blow for the Commission, especially Margrethe Vestager, who has led the EU body's competition enforcement in recent years. 

The original case held that Ireland had effectively granted Apple illegal "state aid" by allowing Apple Sales International (ASI) and Apple Operations Europe (AOE) to be based in Ireland without paying tax. 

Today's ruling overturns that decision, and says the Commission was "wrong to declare that ASI and AOE had been granted a selective economic advantage."

But the ruling is not straightforward. The court said it "regrets the incomplete and occasionally inconsistent nature of tax rulings," but crucially said that in its investigation and original decision, the Commission did not present "sufficient" evidence that Irish authorities gave an advantage that could be seen as illegal under the specific state aid legislation. 

Apple defended the action, saying the income seen by the Commission as taxable in Ireland was international and taxes were paid in the nations where products were sold. 

In reaction to Wednesday's ruling, Apple said: "This case was not about how much tax we pay, but where we are required to pay it."

"Apple has paid more than $100 billion in corporate income taxes around the world in the last decade and tens of billions more in other taxes," the statement added. 

The European Commission is expected to appeal Wednesday's ruling.