EU regulatory guidelines stipulate that such fines are capped at up to 10 percent of the company's global turnover. As part of Alphabet, Google could have been slapped with a charge of up to $9 billion based on its 2016 turnover. While the final bill fell short of this, it eclipses the 1 billion euro ($1.45 billion) fine doled out to chipmaker Intel in 2009. It is also higher than estimates cited by sources in the lead-up to the verdict.
Alphabet's share price dropped 1 percent on the announcement in premarket trading Tuesday.
Alphabet generated $24.75 billion in revenue in the latest quarter, with advertising revenues of $21.4 billion.
Regulators are continuing to investigate two other charges, including whether the Android mobile operating system is being used to promote other Google products at an unfair disadvantage to rivals.
The ruling may also open the way for private litigants to seek compensation for damages at national courts.
"EU antitrust rules apply to all companies that operate in Europe's Economic Area, no matter where they're based," Vestager said. "The purpose is to ensure competition and innovation for the benefit of European consumers. Google has come up with many innovative products, and many innovative services, that have made a difference in our lives — and that's a good thing."
"But Google's strategy for its comparison shopping service wasn't just about attracting customers. It wasn't just about making its product better than its rivals. Google has abused its market dominance in its search engine by promoting its own shopping comparison site in its search results and demoting its competitors."
Google, which makes most of its money from advertising, has argued that the European Commission's theory "just doesn't fit the reality of how most people shop online."
"They reach merchant websites in many different ways: via general search engines, specialist search services, merchant platforms, social media sites, and online ads served by various companies," Kent Walker, Google's general counsel, said in a blog post.
"And of course, merchants are reaching consumers directly like never before. On the mobile web — and more than half of Europe's Internet traffic is mobile these days — dedicated apps are the most common way for consumers to shop."
— Reuters contributed to this report.