And in tearful scenes outside the club's Stade de la Beaujoire on Friday morning a 'keep hope' banner was removed in front of the floral tribute.
On Wednesday, it emerged an unidentified body - now known to be Sala - was brought off ship, Geo Ocean III, on a stretcher and transferred to a private ambulance before being taken to Dorset Police and the local coroner.
The plane was flying from Nantes, France, the home of Sala's former team, to Cardiff on January 21, when it crashed into the sea with the new £15million signing and pilot David Ibbotson inside.
The French club released a heartfelt statement on Friday, confirming the decision to retire the shirt.
'FC Nantes had the immense sadness on Thursday to learn that the body found was that of Emiliano Sala. This news puts an end to interminable and unbearable waiting. Emiliano will forever be on the legends who has written the great history of FC Nantes.
'There are difficult mornings, nightmarish awakenings, where unhappily relity hits us. Emis is gone...
'Emiliano Sala arrived on the backs of the Edre in July 2015 and knew how to win the hearts of the Nantes supporters.
'With his work, his desire and his kindness without limits, he finished as the club's top scorer in his three seasons.
'The homages paid to him nationally and internationally match the player and personal that he was.
'Today, we have lost a friend, a talented player and an exemplaray team-mate.
'We can't forget in this drama the pilot and his family and have confidence that the authorities will continue their search.'
Waldemar Kita, president of Nantes said: 'I don't have the words. It's a tragedy, I'm crushed. Emiliano left his mark. That's why, like many fans, I wish to honour him by retiring the No 9.
'Nantes, its board, its staff and its players, wish to pass the families of Emiliano Sala and David Ibbotson their deepest condolences. We will never forget you, Emi.
'He's an Argentine who never gives up, Emiliano Sala, Emiliano Sala...'