The region's fishermen have already used up the entire 2010 quota halfway through the year.
"The closure of the purse seine fishery is necessary to protect the fragile stock of bluefin tuna and to ensure its recovery," the commission said.
An international conference on trade in endangered species was held in the Qatari capital of Doha last March when over 40 countries tackled issues such as a ban on export of the Atlantic bluefin tuna.
However, Japan and other Asian nations blocked UN efforts to declare the fish an endangered species, which would effectively ban any international trade for the tuna.
Major tuna fishers France, Greece and Spain were also informed of the EU's decision.
While only a handful of French ships and one Greek ship are still out at sea, their capacity to catch is vast. Spanish ships are reportedly already heading back to port. The French fleet has reached over 85 per cent of its quota.
Oliver Knowles, a Greenpeace International oceans campaigner, said in a statement released on Wednesday: "Bluefin tuna is on the brink of extinction and fishing should never have taken place this year – yet another example of how politics have failed our oceans and the Mediterranean.
"Scientists have shown that the only appropriate fishing quota for bluefin tuna is zero. These ships should not have been allowed to fish at all this season," he said.
Greenpeace estimates that over 80 per cent of the bluefin tuna have already been taken from the world's waters and the species could disappear if fishing is not halted immediately.