Delta Blues, trained by Katsuhiko Sumii and ridden by Yasanuri Iwata, prevailed in a stirring finish from Damien Oliver's mount Pop Rock, also trained by Sumii.
Maybe Better did best of the locals for third.
Iwata could not contain his glee, shouting: "Very happy, very happy.
"My biggest winner ever."
It was the first Cup success by a Japanese raider.
Delta Blues enjoyed the run of the race in second and third place throughout as Zabeat set the pace with Irish topweight Yeats moving up to challenge on the turn.
Yeats momentarily hit the front but Delta Blues soon raced past him and then held off the determined challenge of Pop Rock who tried valiantly but just missed.
Japanese racing
The result proved what many in the racing business already knew that Japanese thoroughbreds lead the world.
At Flemington they led home a field that included the best stayer in Europe, the best in Australia and whatever New Zealand could offer.
It was only the second time a Japanese horse had run in the Melbourne Cup, Eye Popper having finished 12th in last year's race after being second in the Caulfield Cup.
Best of the rest
The best the locals could do was third with Maybe Better, who finished 4-1/2 lengths behind Pop Rock who was ridden by local jockey Damien Oliver.
Oliver said the result was terrific for Japanese racing.
"I had a couple of seasons there and I was pleased to be offered this ride," he said.
"They have very good horses over there.
"It's a fantastic feat for the Japanese to come here and do that."
For the remaining internationals, the race provided mixed results.
The English horse Land 'N Stars ran the best of them, finishing fifth, Irish champ Yeats was seventh and Glistening from England ran 10th.
Another English horse, Geordieland, finished 18th having suffered a bleeding attack during the race.
The joint favourite Tawqeet never got into the action and trailed in a poor 19th.