In particular, EON would acquire control of Endesa Europa, which controls Endesa's activities in France, Poland, Italy and Turkey, and of certain minor activities of Endesa in Spain.
After examining the deal, "the proposed transaction would not significantly impede effective competition in the European Economic Area or any substantial part of it," the European Commission said in a statement.
The deal for EON to pay €11.8 billion for the Endesa energy assets is part of an arrangement that ended its bid for the Spanish group as a whole.
EON dropped its bid for Endesa in April 2007 following a battle of more than one year against Spanish government opposition in exchange for an agreement that allowed the German firm to buy major assets in return.
The Commission had already authorized the proposed Endesa transaction last August.
However in March the initial agreement was modified, obliging the EU authorities to review their decision, which remained unchanged.