Apple's head lawyer fired a salvo at Vestager, the Danish politician who has been the Commission's competition commissioner since 2014, in an interview with news agency Reuters.
“Apple is a convenient target because it generates lots of headlines,” Apple general counsel Bruce Sewell said. “It allows the commissioner to become Dane of the year for 2016.”
Sewell's jab at Vestager was in reference to her selection as the ‘Dane of the Year' by Berlingske newspaper last month.
In her time as competition commissioner, Vestager has aggressively gone after major corporations like Apple, Google, Starbucks, Fiat and Russian oil giant Gazprom.
In August, the European Commission ordered iPhone maker Apple to reimburse a record €13 billion ($14 billion) in unpaid taxes in Ireland.
Led by Vestager, the EU accused Ireland of giving Apple a secret tax deal that allowed the iPhone maker to enjoy near zero tax on its huge sales worldwide for more than a decade.
The deal was in breach of the EU's state aid rules, Vestager argued.
"It's been clear since the start of this case there was a pre-determined outcome," a spokeswoman for Apple told AFP, confirming the appeal.
"The Commission took unilateral action and retroactively changed the rules, disregarding decades of Irish tax law, US tax law, as well as global consensus on tax policy, that everyone has relied on," she added.
Apple's appeal, lodged at an EU court in Luxembourg, came after the bloc's anti-trust teams released their full 130-page argumentation in the case.
"The Commission will defend its decision in court," the Commission said in a short statement, describing a court process that could take years.
With the release, the Irish government also laid out its arguments against the EU case, accusing Brussels of a major breach of national sovereignty.
"The Commission has exceeded its powers and interfered with national tax sovereignty," Ireland's finance department said in a three-page outline of its main arguments.
"The Commission has no competence, under state aid rules, unilaterally to substitute its own view of the geographic scope and extent of the member state's tax jurisdiction for those of the member state itself," the ministry added.
In August, the EU verdict shocked the business world and infuriated Apple, with CEO Tim Cook calling it "political crap".
It also raised tensions with Washington, which accused Brussels of "disproportionately" focusing on US corporations.
"We continue to believe the Commission is retroactively applying a sweeping new state aid theory that is contrary to well-established legal principles," the US treasury said in a statement.
By the Commission's calculations, Dublin allowed Apple to pay a tax rate of 1 percent of its European profits in 2003 which then dropped to 0.005 percent by 2014.
Ireland formally lodged its appeal in November after winning the backing of the Irish parliament, with MPs willing to forgo the decision's potential windfall in order to preserve Dublin's pro-business reputation.
Apple -- with 6,000 staff in its Cork city campus -- is a valued employer in Ireland where it has had operations since 1980.