Top Cellar, in Easter Road, had a haul of 1500 bottles of posh vintage worth around £35 each.
But the owners claim they did not realise their 100 boxes of high-quality Burgundy had been stolen.
They sold the bottles for around £6.99 each before a member of the public realised its value and became suspicious.
Trading Standards and Lothian and Borders Police swooped on the shop and found the haul, which was bought in Dover in April.
The stash included bottles of Chablis Sancerre and Grand Cru Chablis by Jean-Marc Brocard.
It is understood that the owners did not realise the value of the bottles was about £52,500 and so set a price tag of only £6.99.
James Wrobel, 38, who owns a nearby independent wine shop, said the bottles seized were a top brand.
He said: “Brocard is a very posh name in the world of Burgundy. It is a big luxury brand and they generally create the highest level of Chablis. I couldn’t believe it when I heard. They [Top Cellar] clearly did not know how valuable it was. Generally, if a deal seems too good to be true, it probably is.”
It is not the first time large stocks of wine have been uncovered in the city.
In February 2010, family-run Granton Food & Wines was found to be selling bottles of vodka that had been among £900 worth of alcohol stolen from the Asda supermarket at Sandpiper Drive.
A director of the West Granton Road store admitted to buying the stock for around £10 a bottle from an individual who visited the shop and claimed he was selling the bottles cheap because the labels were damaged.
In August 2011, stores across the city were being checked by police after officers found fake bottles of wine for sale in a store in Leith.
A police spokesman said: “Lothian and Borders Police and Trading Standards officers seized a large quantity of stolen wine from a licensed premises in the Leith area of Edinburgh during a joint agency investigation in April.
“Over 100 boxes of bottled wine, which had been stolen from a port in Dover, were seized and the premises is now subject of a report to the licensing board.
“A 41-year-old man and a 32-year-old woman have now been reported to the procurator fiscal in connection with these inquiries.”
Nobody from Top Cellar was available for comment.