The plan sets binding quotas for the member states to take in the 120,000 refugees who are currently in limbo in countries like Hungary, Italy and Greece.
Swedish Justice and Migration Minister Morgan Johansson, who already said before the meeting that he would push for a mandatory resettlement plan for asylum seekers, has welcomed the final decision. Sweden will receive some 4,300 refugees, mostly from Italy and Greece.
"This distribution is binding, and mandatory in that sense. No member state can buy its way out of this. The previous proposal about this is gone," Johansson tells Swedish Radio News.
He explains that if a country fails to follow the directives, it could end up in court.
"Of course, if that is the case, then the European Commission would have to act against that country. And that is done in court," Johansson says.
Czech Republic, Slovakia, Romania and Hungary voted against the plan and Finland abstained, but the decision will affect them too.
Europe's leaders are expected to discuss Hungary's handling of the refugee crisis during the last weeks, after several media reports accused the country of using tear gas and water cannons against asylum seekers trying to cross its borders.
An aid package for the refugee camps in Turkey, Lebanon and Jordan is also on the agenda for the meeting.
A sensitive issue that will be discussed is the border controls many EU countries have started performing within the Union, which is against the free movement of people guaranteed by the Schengen agreement. Austria, Germany, Hungary and Finland have imposed identity checks on their frontiers with certain countries.