Almost immediately after the earlier ransom drop, a Singapore-flagged Indonesian chemical tanker and its 24-strong crew were released by the pirates, Commander John Harbour, a Navfor spokesman, told AFP.
The pirates disappeared back to the shore of impoverished Somalia.
Navios Apollon is the latest freighter to be involved in a ransom drop in the Indian Ocean, following its capture in late December while it was en route to Thailand.
The ship's captain is Greek and the crew is Filipino.
The EU statement said that "no requests for assistance have been made at this time" and Navfor was continuing to monitor the situation.
According to Harbour, it normally takes up to 24 hours for pirates to release the ship and crew "after the money has been counted".
Somali pirates, targeting one of the world's busiest maritime trade routes, raked in an estimated 60 million dollars in ransoms last year.
They currently hold five vessels and some 120 seafarers, according to Harbour.
The EU Navfor mission is tasked with escorting merchant vessels carrying humanitarian aid and protecting vulnerable ships in the Gulf of Aden and Indian Ocean.