This would not be a problem if there were several big search engines.
But Google's market share in most European countries exceeds 90%.
When the firm introduced the changes, traffic to rival websites, such as Britain's Foundem, plunged.
This denied other firms the chance to compete and reduced consumer choice, said Ms Vestager.
Google has 90 days to find a way to treat its own comparison-shopping service and those of rivals equally.
Predictably, Google wants none of this.
It says its search service is far less dominant than it appears: consumers look up products on many other sites, including Amazon and eBay (the commission did not count these as search engines).
Google also notes that the changes made in 2008 benefited consumers.
“People usually prefer links that take them directly to the products they want,” Kent Walker, the firm's general counsel, wrote in a blog post.
Here, Google appears to have a point.
Why would consumers want to click on a link which leads them to another site if they can see products and prices neatly lined up above Google's search results?
The European Court of Justice, the EU's highest court, will have to weigh the merits of its argument.
Google will appeal, and there are weaknesses in the commission's case, such as the difficulty of proving real consumer harm from the treatment of other price-comparison sites.
Yet the commission deserves credit for tackling a question, which is increasingly important but which American trust busting agencies have avoided: what is the responsibility of dominant online firms, including Amazon and Facebook, when direct competitors, large and small, offer products and services on their platforms?
The prevailing wisdom, particularly in America, used to be that “super-platforms”, despite their size, do not unfairly use their market power and thrive because of their unceasing innovation.
The competition is always just one click away, argues Herbert Hovenkamp of the University of Pennsylvania.