Ms. Vestager said that she could not say how much Apple had ultimately received from Qualcomm in payments, but that it was in the “billions of dollars.”

She said that internal documents reviewed as part of the inquiry showed that Apple had seriously considered using chips made by a rival manufacturer, Intel, during the period of its agreement with Qualcomm, but did not do so until the deal with Qualcomm had concluded.

If Apple had introduced a smartphone using products from a different chip maker, she said, Apple not only would have lost future payments from Qualcomm, but also would have been forced to pay back some of the money it had already received.

Ms. Vestager said that Apple would not face any repercussions because the inquiry had been focused on Qualcomm’s practices. European regulators are also continuing a separate investigation into preliminary findings that Qualcomm sold its chips at below cost price from 2009 to 2011 to force a competitor out of the market.

In a statement, Qualcomm said that it “strongly disagrees” with the decision and that it would appeal the ruling to the European Union’s highest court.

“We are confident this agreement did not violate E.U. competition rules or adversely affect market competition or European consumers,” Don Rosenberg, Qualcomm’s general counsel, said in a news release. “We have a strong case for judicial review, and we will immediately commence that process.”

The fine on Wednesday came with Qualcomm in the midst of multiple takeover battles. It has sought to fight off a hostile $105 billion takeover attempt by a rival, the Singapore-based chip maker Broadcom. If completed, that takeover would be the largest technology deal in history. And despite that battle in the background, Qualcomm is still looking to complete a $38.5 billion acquisition of NXP Semiconductors.