After suffering from an infection, St Mark's Basilica still had an Arc entry but the saintly Irish Champion Stakes winner will now take on a lucrative stud career.
The three-year-old, winner of last year's Dewhurst, bows out unbeaten in four starts this term having landed the French 2000 Guineas and Prix du Jockey Club, plus the Eclipse at Sandown and the Irish Champion Stakes on his most recent outing earlier this month.
Trained by Aidan O'Brien for the Coolmore team, the son of Siyouni will stand at their stud next season.
"St Mark's Basilica is possibly the best horse we have ever had in Ballydoyle," said O'Brien.
"He relaxes and quickens and has all the determination from Galileo and all the speed from Siyouni."
Coolmore's David O'Loughlin added: "He's the most exciting prospect we've retired from Ballydoyle since his late grandfather Galileo.
"European Champion Two-Year-Old, the highest-rated three-year-old in the world, a 1,300,000 guineas yearling by a top sire in Siyouni, a half-brother to another brilliant horse in Magna Grecia, both out of Galileo's group-winning two-year-old Cabaret. He has everything and he'll get terrific support from his owners' broodmare band too."
St Mark's Basilica won six of his nine career starts and won over £2.1million in prize money.