The force has also agreed not to include the product, often associated with violence, in anti-crime bottle-marking schemes unless it has "reasonable grounds" for doing so.
Last year, moves to add labels to the drink to allow officers from the former Strathclyde Police force to trace bottles back to where they had been purchased infuriated Buckfast distributors, who branded it a "form of ethnic cleansing of brands of alcohol that police and politicians don't like".
Lawyers for J Chandler & Co took the case to the Court of Session claiming that the labels were being used illegally and in a way that discriminated against the brand. The two sides have now settled the case almost a year on, without any judgment from the court.
Police Scotland, which took over Strathclyde's responsibilities last April, has now apologised to Buckfast for the actions of an individual officer who tried to stop a retailer from stocking the tonic wine. It also apologised for any "distress or inconvenience" caused to the shopkeeper and, in a written undertaking, Assistant Chief Constable Wayne Mawson said police "will not request licensed retailers to cease stocking for sale Buckfast Tonic Wine".
Jim Wilson, spokesman for J Chandler & Co, said: "We accept the apology and we believe it to be very sincere."
A Police Scotland spokesman said: "We can confirm there has been an amicable settlement between Police Scotland and the owners of Buckfast."