The plan to take sovereign control of the bloc's borders was initially met with resistance from some countries not keen on allowing Brussels the power to intervene without their consent in an emergency.
Polish Foreign Minister Witold Waszczykowski said the replacement of Frontex "by a structure that is independent of member states is shocking."
However, a text of the conclusions following the decision by all member states to sign up to the new border control and coast guard system, said that countries pledged to "deal as soon as possible with weaknesses at the external borders of the Schengen area, ensuring systematic security checks with updated databases and to prevent the falsification of documents."
The European Council (EC) also agreed that all EU countries "ensure systematic and complete identification, fingerprinting, take all necessary measures to avoid registration refusal, and reduce irregular migration flows."
More than 1.2 million refugees have fled to Europe so far this year, which has led to chaotic scenes on many of the bloc's borders. And as the refugee crisis gripped Europe, many migrants refused to have their fingerprints taken on their arrival in countries where they didn't wish to remain.
This led to a movement of people through so-called "irregular" routes, namely the Western Balkan route which surpassed the journey across the Mediterranean Sea to Europe as the most popular for migrants, refugees and asylum seekers.
In defiance of the EU's founding freedom of movement principle and feeling the strain of the European refugee flow, many countries took matters into their own hands and built unofficial walls and wire fences to keep people out.
The decision to build unofficial borders and fences was met with condemnation from Brussels, piling on the pressure for a solution to the crisis.
The EC hopes that the new centralized border force and coast guard unit will protect the Schengen zone, and fundamentally, the founding principle of Europe's freedom of movement — but now with more rigorous checks on migrants.
European Council President Donald Tusk said: "If we fail to protect European Union borders, we would have failed as a political union."