"You're always worried when they pull out in the morning [after a race] and when he pulled out, he was very sore. When he was x-rayed, his sesamoid was coming apart.
"It's incredible that he ran the race that he did really. We're very sorry to lose him, he was an unusual horse who stayed very well but quickened very well.
"When John [Magnier, one of the colt's owners] saw the x-ray, there was absolutely no chance that he would ever race again.
"I was speaking to JP [Magnier] on the way home last night and saying that he was a perfect horse to have a midsummer break and then give him a prep for the Arc. That's the type of horse that we thought he was going to be."
Wings Of Eagles, a son of the 2011 Derby winner Pour Moi, is expected to take up stallion duties at Coolmore Stud next year.
O'Brien reported that his remaining runners in Saturday's Classic, including Capri, "all pulled out fine" on Sunday morning, but also that Minding, the winner of five group one races last year including the 1000 Guineas and the Oaks, will need more time than expected to recover from a setback in the spring.
It also emerged on Sunday that Somehow, the winner of the group two Dahlia Stakes in May, has been put down after suffering an injury on the gallops.
"Somehow got a fracture behind on her cannon bone and we were unable to fix it. It's a real pity as she was such a good filly."