Andrea Atzeni was denied back-to-back Ladbrokes St Legers by the Doncaster stewards after Simple Verse was disqualified and placed second behind Bondi Beach.
Supplemented at a cost of £50,000 on Monday, Simple Verse (8-1) was aiming to become the first filly to beat the boys in the Classic since User Friendly in 1992.
History appeared to have been made when Ralph Beckett's three-year-old crossed the line a head in front of Aidan O'Brien's Bondi Beach (2-1 joint-favourite), but the claxon was sounded due to two incidents of interference inside the final quarter-mile.
Colm O'Donoghue and Atzeni both presented their case in the stewards' room and after a lengthy discussion the placings were reversed, to the displeasure of some in the crowd.
When the winning connections were presented with the famous old trophy and O'Donoghue the Leger cap, boos and the odd shout were ringing out.
Atzeni won in the colours of Paul Smith on Kingston Hill 12 months ago but this time they were on opposite sides, with Smith representing his father, Derrick, part-owner of Bondi Beach.
Immediately after the result was revised, Beckett announced his intention to appeal the decision.
O'Brien, winning the race for the fifth time, said from Leopardstown: "It's never a nice way to win and I'm sorry for the connections of the second.
"It was a bit of a messy race up the straight, I didn't really see it, but he was closing the gap going to the line.
"Obviously I'm delighted and Colm gave him a great ride. I have to thank everybody involved with him. Andrew who rides him and everyone in the yard.
"He was unlucky in York (in the Great Voltigeur behind Storm The Stars) when he got two proper bumps and was carried right across the track.
"Some days these things fall your way and some days they don't.
"I'm sorry for the connections of the second.
"It's only his fifth run, he loves fast ground and he stays well. He'll be a lovely horse next year."
O'Donoghue, banned for two days (September 27 and 28) for using his whip above the permitted level, said: "It's racing, we all want a fair shot at it, I had time (after first bump) to go and get him (Atzeni), but again I got impeded.
"My momentum was stopped, all I know is I tried to have a fair shot at it. I got impeded, and the rules have made the decision today.
"It's important to win my first St Leger. I need this, I want this and I'd like to thank the owners and Aidan for giving me the chance."
Beckett, whose Secret Gesture was recently demoted to third after being first home in the Beverly D. Stakes at Arlington in the same colours, said: "I'm astonished, apart from anything else. There's no consistency in the rules.
"We saw Stuart Williams' horse Suzi's Connoisseur (in the same Qatar Racing colours) pinned against the rail on the straight track at Ascot last week and Joe Fanning had to stand up in the irons and was beaten half a length but didn't get the race.
"Can you honestly say that it was entirely her fault? Could you put your hand on your heart and say it was her fault in the last half furlong?
"I don't think I can answer that question - can anybody else? One thing is for certain - we will appeal this. That's all I've got to say on the matter."
Atzeni was on Captain Morley in the following Napoleons Casinos And Restaurants Handicap and came home to a bitter-sweet success by four lengths in the Simple Verse silks.
Still extremely upset at having the Leger taken away, the Italian admitted he was crying in the stalls for that race.
He said: "I'm down, still feel low and felt like going home.
"I was crying in the stalls, but at the end of my day it's my job. That's what that's what I get paid for. That's racing.
"It's done, it's over. It's a shame for the boss really (Sheikh Fahad), he deserves a big winner and it's a shame for all the team.
"I'm gutted as I think the best horse won the race. It's hard, but these things happen. What can you do? I didn't think I would lose it, she was the best horse in the race. I gave the winner a little bump, he leaned on me as much as I did him.
"We will have to (appeal), it's a Classic and you can't let that go."
Atzeni was banned for three days for the first incident (September 27 - 29) but the second bump was considered accidental, with the decision made as a consequence of both incidents.
Paul Barton, senior stewards' secretary for the British Horseracing Authority, explained how the panel reached its decision.
He said: "Clearly there was interference and we took the view there were two instances of interference. One inside the two-furlong marker and one inside the half-furlong.
"We looked at each one separately and took the jockeys' evidence.
"Having concluded that both cases of interference came from Simple Verse, the stewards then had to decide if that interference improved that horse's placing over Bondi Beach.
"The combination of the two instances, in our opinion, improved Simple Verse's placing.
"These cases are always hard. We try to take a dispassionate view. It's a refereeing decision. We make it on sound principles.
"Whether it's unanimous or not we never say, but in the room the decision the stewards have to take is whether they are satisfied.
"They have to leave the room feeling comfortable that the decision they made is a correct one and I believe it was."
The other 2-1 joint favourite, Storm The Stars, was close up in fourth, with jockey Pat Cosgrave and trainer William Haggas suggesting he failed to see out the trip and that he has probably run his last race this season.