Concerns over the pair’s behaviour were raised at Glasgow Airport just before their Air Transat A310 with 250 passengers on board was due to depart for Toronto on 18 July 2016.
Canadians Jean-Francois Perreault, 41, and Imran Syed, 39, were arrested before they were due to take off.
Mr Syed, from Toronto, was accused of performing “an activity ancillary to an aviation function” when he allegedly had 49mg of alcohol in 100ml of blood, more than double the legal limit of 20mg.
Mr Perreault, from the province of Ontario, faced the same charge with an alleged 32mg of alcohol in 100ml of blood.
They had denied the charge.
At a previous hearing, which could not be reported until now, Paisley Sheriff Court heard that both men requested part of their blood samples when they were taken in July 2016 so that they could have them independently analysed.
The samples were among their belongings when they arrived at HMP Low Moss on 19 July 2016.
Paul Scoular, security manager at the prison, working for the Scottish Prison Service, said he was concerned the blood samples were redundant as they had not been in cold storage.
Mr Scoular said both men gave him their consent for the samples to be destroyed, which they duly were.
However, when giving evidence, Mr Perreault said he did not give permission for his blood sample to be destroyed.
The court ruled that the case could proceed because samples had been made available. It added that police and the Crown were not responsible for what happened to them later.
This was contested by the defence – and the Appeal Court subsequently ruled the Crown had not met its duty to supply the pilots with their part of the blood samples.
On Thursday, the case formally was dropped.
A Crown Office spokesman said: “After full and careful consideration of the facts… Crown Counsel instructed there should be no further proceedings at this time.
“We are working with Police Scotland to ensure there are proper processes and guidance in place covering the retention and storage of samples when an accused person is remanded in custody.”
Both men were suspended by Air Transat after their arrest but will be meeting with the airline to plan their potential reinstatement. The pair will be required to undergo retraining and requalification.
The airline, which says the safety of their passengers and flight crews is their number one priority, stated: “We will be meeting with them in the next few days to plan their reinstatement since there is no charge against them and we have no evidence that they have broken any law nor our internal rules.
“They will need to undergo retraining and requalification as per applicable legislation, and we will put in place measures to ensure that their behaviour is exemplary.”