It gave the company 90 days to comply or face further fines. The company last week confirmed that it would comply, and the fine will be paid into a frozen account pending the appeal.
The commission said that since 2008, Google has systematically given prominent placement to its own comparison shopping service, while demoting rival comparison shopping services in its search results.
Following the ruling, Google said it "respectfully" disagreed and was considering whether to appeal.
The Commission is reviewing its Google Shopping decision in light of the ECJ's Intel ruling, according to Reuters. A court spokeswoman said Google has not asked for an interim order to suspend the decision to levy an fine.
A court battle between Brussels and Google could take years to resolve and adds to an increasingly bitter row between the USA giant and European countries.
"What Google has done is illegal under EU antitrust rules", EU Commissioner Margrethe Vestager at the time.
"The commission will defend its decision in court", a spokesperson for the commission said. "And most importantly, it denied European consumers a genuine choice of services and the full benefits of innovation".
Google took its fight over a record European Union antitrust fine to the EU courts, starting a legal challenge that could take years to conclude.
The EU fined the internet giant for abusing its dominance in Europe to position its own shopping comparison service at the top of Google search results. The first relates to Android, its operating system on a smartphone, and the second AdSense, its advertising network.