But in 2016, Facebook released an update to its terms of service that raised the possibility of linking accounts from both platforms.
"By coordinating more with Facebook, we'll be able to do things like track basic metrics about how often people use our services and better fight spam on WhatsApp," the messaging firm said in a blog post at the time.
"And by connecting your phone number with Facebook's systems, Facebook can offer better friend suggestions and show you more relevant ads if you have an account with them."
But the Commission said that contrary to Facebook's statements in 2014 saying it wasn't able to link accounts, the U.S. firm was aware that such a possibility existed.
However, the fine will not impact the EU body's previous decision to approve the acquisition.
"The Commission at the time also carried out an 'even if' assessment that assumed user matching as a possibility. The Commission therefore considers that, albeit relevant, the incorrect or misleading information provided by Facebook did not have an impact on the outcome of the clearance decision," a Commission statement read.
It added that Thursday's fine is unrelated to any ongoing national antitrust or data protection issues that may arise following the update that WhatsApp rolled out in 2016.
Facebook said that to the best of its knowledge, the information it provided was correct.
"We've acted in good faith since our very first interactions with the Commission and we've sought to provide accurate information at every turn. The errors we made in our 2014 filings were not intentional and the Commission has confirmed that they did not impact the outcome of the merger review," a Facebook spokesperson told CNBC by email.
"Today's announcement brings this matter to a close."