The five-year-old mare was one of five horses to test positive for the substance in their 'A' samples in July.
Buckingham Palace and the horse's trainer, Michael Stoute, claimed that the positive test came as a result of feed product being contaminated.
Estimate came first during the 2013 race and will be stripped of the second-placed finish from this June after the British Horseracing Authority (BHA) confirmed the disqualification on Thursday.
The prize money for the runner-up spot will now to Missunited, which finished third on the day.
The BHA announced on their official Twitter feed: "Result of Disciplinary Panel hearing re: positive samples detected in Estimate and Russian Realm (Sir Michael Stoute) at Royal Ascot.
"The horses have been disqualified from the races in question. No financial penalty has been imposed upon the trainer.
"The hearing involving four other trainers is ongoing. Official notices and BHA statement to be published in due course."