Dubai Millennium died last night following a week-long struggle against Equine Grass Sickness.
The 2000 European horse of the year was five years old.
In a statement, John Ferguson, Sheikh Mohammed’s bloodstock adviser, said: Dubai Millennium became uncomfortable on Sunday night, and it was evident that a third emergency surgery was necessary.
Ferguson explained: "It soon became clear that there were complications of the intestinal tract that were inoperable.
"His prospects were hopeless and, on humane grounds, Dubai Millennium was not allowed to recover from the anaesthetic."
In 1999, Dubai Millennium proved himself Europe's top three-year-old miler with wins in the Queen Elizabeth II Stakes and Prix Jacques le Marois.
At Epsom, however, he appeared not to stay the mile-and-a-half trip in the Derby. Sent off favourite he could finish only ninth, suffering what turned out to be the only defeat of his career.
But Dubai Millennium proved himself a world-beater over 10 furlongs last year. He ran away with the 2000 Dubai World Cup and put up a breath-taking display to land the Group One Prince Of Wales's Stakes at Royal Ascot.
But just as a match with French champion Montjeu was being planned last August Dubai Millennium fractured a leg on the gallops and had to be retired.
He went to stud the winner of nine career races and Stg£2.75 million in prize money.
Dubai Millennium had covered a reported three-quarters of his first book of mares when he was struck down by the grass sickness.He will be buried in the stallion graveyard at Sheikh Mohammed's Dalham Hall Stud.