Alkaased held off Heart's Cry in a photo finish to give jockey Frankie Dettori the third Japan Cup victory of his career.
Alkaased (left) and Heart's Cry battle it out over the closing stages
The Luca Cumani-trained Alkaased just edged out Christophe Lemaire's fast-finishing mount to take the Group One race in Tokyo.
Last year's winner Zenno Rob Roy was third, with Lincoln fourth and the Ed Dunlop-trained Ouija Board fifth.
It took several minutes for the result of the photo finish to be announced, and there was a further wait as the stewards held an inquiry.
But the result gave Dettori his hat-trick after wins on Singspiel in 1996 and Falbrav in 2002.
The 2003 winner Tap Dance City set a furious pace with Stormy Cafe early on as the pair pulled four lengths clear of the field.
Tap Dance City turned for home with a three-length lead, but was swallowed up by the pack, with Kieren Fallon making a well timed run on Ouija Board.
But Alkaased took a narrow lead in the final furlong and held on to take victory in a record time of two minutes 22.1 seconds for the mile and a half race.