EU competition commissioner Margrethe Vestager filed the case against Ireland for having failed to recover the outstanding amount, Reuters reported.
Apple paid the first instalment in May, depositing €1.5 billion (US$1.76 billion) in an escrow account set up for this purpose.
The fine was imposed on Apple in August 2016 with the EU claiming that a number of deals the company had struck in order to do business in Ireland were illegal.
Both Apple and Ireland have appealed the verdict, a process that may take as long a five years. The first tranche of the fine was due in January 2017 and in October 2017, the European Commission said it was taking Ireland to the European Court of Justice over delaying the payment.
Apple and Ireland reached agreement over what was deemed a suitable escrow arrangement in December 2017. In March, Ireland put Amundi, BlackRock Investment Management and Goldman Sachs Asset Management in charge of the escrow account and gave them authorisation to make low-risk investments that would not put Irish taxpayers at risk.
Commission spokesman Ricardo Cardoso told Reuters by email: "In light of the full payment by Apple of the illegal state aid it had received from Ireland, Commissioner Vestager will be proposing to the College of Commissioners the withdrawal of this court action."
Graphic: courtesy the European Union