Gentildonna has failed in her bid for a third Japan Cup, finishing fourth behind Epiphaneia.
The race was marred by the death of Godolphin's Trading Leather who had to be euthanised after breaking a leg.
"Trading Leather was much adored and had a tremendous career, the highlight being his Irish Derby win," Trading Leather's trainer Jim Bolger said on Godolphin's website.
"His passing is tough for us all, especially my staff. This is a very sad loss."
Winning trainer Katsuhiko Sumii was pleased to see Epiphaneia live up to the promise he showed when he won last year's Japanese St Leger.
"I am relieved and happy that Epiphaneia was able to prove what he can do today, because despite showing his outstanding potential in winning the Kikuka Sho, he hadn't been able to race like we'd hoped," he said.
"He has so much energy, which can really be hard to control, so I knew that the key to his winning was whether you can preserve that energy to the stretch."
Christophe Soumillon was able to do that with Epiphaneia finishing four lengths clear of Just A Way.