Master The World was awarded the Betway Winter Derby in the stewards' room after Mr Owen crossed the line first at Lingfield.
Jamie Spencer looked to have done everything right on David Simcock's Mr Owen, delivering his challenge late on as he surged past last year's winner Convey.
However, the David Elsworth-trained Master The World (16-1) was coming with a real rattle down the outside under Sean Levey.
As the post approached, Mr Owen veered markedly out to his right and into Master The World's path, with Levey seemingly forced to stop riding for a couple of strides.
The winning margin was a head, but the stewards felt the interference was enough to alter the result and reversed the placings.
Battle Of Marathon outran his 33-1 odds in third, but Aidan O'Brien's favourite, Clear Skies, never got involved.
Kevin Quinn, who owns the winner in partnership with Chris Benham, said: "Master The World came from nowhere and would have won but for the bump.
"He will come back for the Betway Easter Classic on Finals Day (March 30) and would have a live chance based on that performance.
"Sean Levey gets on so well with him and having the right jockey on board massively helps. Sean wasn't on board last time and, because they have such a good connection, we probably shouldn't have run him. It is important to maintain those relationships when a horse and jockey get on so well.
"He is a great horse and Sean is a genius in the saddle. He's a top jockey and David Elsworth will continue to pick Sean where he can. The team have done a great job with him and credit where credit is due."
Benham added: "We adore the sport as owners and Master The World has been such a stalwart for us so we will continue investing in the sport and we would love another horse like this."
The stewards found the interference in the closing stages to be accidental and Simcock added: "He (Mr Owen) spooked at a shadow close home or else he would have kept straight."
The performance of Clear Skies was considered by the stewards, with O'Brien's representative reporting "the filly was unsuited by the downhill section of the track, running into a tight bend."