Newmarket's on-course vets said Gray Pearl was put down after suffering an "apparent spinal chord injury" in an awful incident before the Qipco 1000 Guineas.
The second Classic of the season was delayed for nearly 30 minutes after the Charlie Hills-trained filly tried to escape beneath the starting stalls and became stuck.
Gray Pearl could not be moved for some considerable time, despite the best efforts of the stalls handlers, and was taken away in a horse ambulance.
A decision was then taken by racecourse vet Simon Waterhouse and Chris Hammond, the attending BHA veterinary officer, to put her down.
Hammond said: "Gray Pearl went down in the stalls and incurred an injury in the process.
"On examination by the racecourse vet, it became evident that she had lost the use of her hind legs and was suffering from an apparent spinal chord injury.
"To minimise distress to the filly, a decision was made to have her put down on welfare grounds.
"This decision was taken after consultation between myself and the racecourse vet."
Amy Starkey, managing director of Newmarket Racecourses, said: "We are extremely saddened by what happened to Gray Pearl.
"Our sympathies are with all the connections of the filly."
Hills described Gray Pearl's death as "a terrible shame and very sad".
He said: "We think maybe she hit her back in the stalls
"She moved beautifully down to the start but then, suddenly, she went down under Michael (Hills). It's a terrible shame and very sad."