The new rules are designed to bring outdated copyright regulations into the online age, making internet platforms liable for content uploaded to their sites.
A total of 19 European Council members, including France and Germany, voted in favour of the new Copyright Directive.
Italy, Luxembourg, Netherlands, Poland, Finland and Sweden voted against adopting the directive, whereas Belgium, Estonia and Slovenia abstained.
The directive includes the controversial Article 11 and Article 13 (now renamed Article 17). Article 11, dubbed the link tax, requires news aggregators and others to pay a charge when they link to certain articles on the web. Article 17 will require online platforms such as YouTube to filter or remove copyrighted material from their websites.
Supporters claim the rules are required to ensure that music companies and news outlets are properly paid for the content that technology companies distribute. But opponents, who assembled in force, allied with those tech firms to argue that it could change the way the internet works and destroy some of its fundamental principles.
Critics including Google, fear a surge in takedown requests could turn the web into a ghost town. Internet campaigners, meanwhile, have warned that the resulting censorship could quell unique forms of online expression, from GIFs to memes.
EU countries now have 24 months to apply the directive to their national legislations.