The article you posted states that Apple won their appeal against the finding of illegality in the ECJ.
Taxation is not an EU competence so in general it is not within the power of the EU to declare a member state's tax policy to be illegal. Vestager has been trying to use state aid as a vehicle to circumvent that restriction but the ECJ rebuffed her attempt to do that in Ireland. A big part of the problem is that the state aid findings rely on the assertion that tax authorities applied special rules to one particular company, which is typically not the case.