Godolphin's Cross Counter, ridden by Kerrin McEvoy, won the 158th running of the Aus$7.3 million (Dh19m) Melbourne Cup at Flemington racecourse on Tuesday.
Marmelo finished second in the two-mile handicap, with A Prince Of Arran third.
It was the first time Godolphin have won the "Race that stops a nation" and caps a stunning 2018 for the Dubai racing operation headed by Sheikh Mohammed bin Rashid, Vice President and Ruler of Dubai.
Thunder Snow won the Dubai World Cup in March and Masar, trained by Charlie Appleby, gave the famous blue silks their first victory at the Epsom Derby in June.
"This is everybody's dream," said winning trainer Appleby of Cross Counter's victory. "This year has been so incredible, winning a Derby and now this. I don't want it to end.
"For me it's obviously very special to be here, but for the team, it's just fantastic. I've spoken to His Highness [Sheikh Mohammed] and he's over the moon about this result - it's a challenge that's been a long road.
"I can't thank everyone enough. It's a day I will never forget. It's been a very memorable day."
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Torrential rain pelted down on Melbourne in the morning, causing chaos at the racecourse where train-loads of spectators were held up from alighting at the nearby station.
But the weather cleared after midday, buoying a festive crowd and drying out the track from heavy to soft an hour before the race.
Saddled with 51kg, the equallest lowest burden with Rostropovich, Cross Counter had work to do entering the final turn after jumping wide from barrier 19.
Runaway set the early pace in the two-mile contest, with McEvoy content to sit towards the rear of the field and he had only a handful of horses behind him turning for home.
He had to switch wide to launch his challenge in the straight, with the Charlie Fellows-trained Prince Of Arran having set sail for home.
However, Cross Counter was flying in the final furlong and while Marmelo also tried to produce a winning sprint, he had no reply to McEvoy's mount.
The Aidan O'Brien-trained Rostropovich finished fifth, but fellow Ballydoyle inmate Cliffs Of Moher sadly broke down passing the post for the first time.
McEvoy said: "What a thrill - to do it for Sheikh Mohammed and Charlie Appleby. Obviously Godolphin has been a huge supporter of mine. Well done to Charlie and this little horse.
"I was back a little bit further than I wanted, I knew I was full of running and at the furlong I thought 'is this happening again?'. I'm just lucky I can ride light and he's been unbelievably well prepared by Charlie Appleby."
But there was sadness among the 100,000-strong crowd with Irish five-year-old The CliffsofMoher, ridden by champion jockey Ryan Moore, euthanised after suffering a fractured right shoulder early in the race.