The vessel had been sighted earlier carrying a ladder and up to 20 fuel drums, 180 miles east of the archipelago islands of Socotra, and was clearly planning to attack a merchant ship.
Operation commander of the EU Naval Force, Rear Admiral Potts, said: "This was the first sighting of a suspect pirate vessel in the Somali Basin for over three months, and EU Naval Force got to it before it had a chance of carrying out an attack on ships transiting the are.
"We knew, as the monsoon period ended this month that pirates would try their luck at sea and this is why we have constantly warned against complacency.
"My message to the pirates is clear: we are watching you and we plan to capture you if you put to sea."
He said the incident had been an indication that pirates still intended to get out to sea, and added: "All involved in countering piracy, whether they are the military or industry must remain vigilant and prepared."
EU NAVFOR said the skiff had been destroyed, "thus preventing the suspect pirates from using it to attack ships in the future".
Naval patrols and counter-piracy measures such as the deployment of armed onboard security teams have reduced successful hijackings in the Horn of Africa region to almost zero.
Nevertheless there are still around 10 vessels and an estimated 250 seafarers held hostage by Somali pirates.