Sheikh Mohammed had been trying for 30 years to win "the race that stops a nation", with Faithful Son Godolphin's first runner 20 years ago.
The Cup dates back to 1865 and was the result of a rivalry between two horse race organizing committees - the Victorian Jockey Club and the Victorian Turf Club, with the latter introducing the event as a handicap race.
"The time difference has meant a lot of punters' activity has come through later in the morning and has been skewed towards the outsiders", the agency's Ella Zampatti said.
Kerrin McEvoy's historic ride on Cross Counter in the Melbourne Cup may have come at a big cost, after making a stunning promise to his wife Cathy before the race.
It was later revealed the horse had suffered a broken right shoulder and couldn't be saved.
Melbourne Cup day has proved a lethal undertaking for runners in recent years, with six horses killed after complications since 2013.
"For me, it is a very special to be here, but like I say, for a team it is just fantastic for everybody".
A cut leg foreleg nearly derailed the Melbourne Cup fortunes of Cross Counter but trainer Charlie Appleby's confidence grew after a track gallop at Werribee a week out from the race.
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Racing out of barrier 19 on a rain-affected track, Cross Counter put on a withering burst of speed down the finishing straight to edge fellow British horses Marmelo and Prince of Arran and win Aus$4 million. I'm just delighted that I can repay his Highness Sheikh Mohammed for putting me in this position, and trusting me in the position to do what I'm doing.
Speaking afterwards, Appleby said: "This is everybody's dream". "It was the Derby and the Melbourne Cup so I'm just so thrilled to have been able to do that".
Appleby credited Sheikh Mohammed and his powerful global stable for the win, saying "they were all family".
"I did promise (the kids) a swimming pool", McEvoy said.
Appleby said Cross Counter ate up after the race and his legs were clean, a good sign of no long lasting effects of the victory.
The Cliffsofmoher's death follows several other tragic incidents in recent years on Cup day.
"It's heartbreaking to see another horse needlessly lose its life during the Melbourne Cup", senior campaign manager Ben Pearson said in a statement.
Aidan O'Brien fielded three contenders with Rostropovich faring best in fifth, but the race was overshadowed by a fatal injury sustained by Cliffs Of Moher passing the post for the first time.