The antiquity had been illegally plundered from an Iberian era archeological site in the province of Alicante, an Interior Ministry statement said.
Inspectors found it in a cardboard box during a routine search of the shop in the eastern town of El Campello.
"We are not yet aware of the full importance of this discovery, but in 20 years' time we will still be talking about this vase," said Jose Luis Simon, an expert from the cultural heritage service of the Ministry of Culture.
Simon said the piece showed decorative paintwork from the Iberian era that tells the story of a hunter who had managed to kill a wild boar, one of the rituals of the time that proved a youth had attained the status of manhood.
He said that while fragments of vases from this antiquity exist in Spain, this was the first to be found whole, making it "of exceptional value."
Simon said the hunting sequences showed similarities to some found on an ancient Greek vase, known as a crater, in the Vatican museum in Rome.
The Interior Ministry said the inspectors who opened the cardboard box knew right away they were dealing with something out of the ordinary and requested technical backup.
"The technicians did not take long to arrive and issue a report confirming the vase's originality," Simon said.
He said it has been moved to the Alicante Archeological Museum for safekeeping.