The three-year-old was delivered with a perfectly-timed run by Kerrin McEvoy to claim the Group One prize and lead home a famous one-two-three for the raiding party, with Hughie Morrison's Marmelo a length back in second and the Charlie Fellowes-trained Prince Of Arran a further three lengths behind in third.
Cross Counter's win came 30 years after Sheikh Mohammed began his Melbourne Cup quest with Authaal who carried his maroon and white colours in 1988 and 20 years after Faithful Son became Godolphin's first runner.
In 2015 crowd favourite and three-time Cup runner up Red Cadeaux had to be euthanised two and a half weeks after the Cup as a result of complications from an injury suffered in that year's race.
"It is with sadness that we confirm that The Cliffsofmoher had to be humanely euthanised after sustaining a fractured right shoulder during the running of the Melbourne Cup at Flemington", Racing Victoria's executive general manager integrity services Jamie Stier said.
"We were confident we had the right horse coming in".
The Cliffsofmoher's jockey Ryan Moore looks dejected as he walks off the track, while Cross Counter's win in the Melbourne Cup plays on the big screen behind him.
After Enable forced a rewrite of the record books at the Breeders' Cup on Saturday, another Newmarket-based horse made history at the 158th Melbourne Cup during the early hours of this morning.
"I've never seen anything like it to be perfectly honest", said the 23-year-old, a junior assistant trainer to his father John who has Muntahaa in the race.
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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.
"He was delighted", Appleby said on Wednesday.
Looking for wet-tracker in this year's Melbourne Cup?
McEvoy said: "What a thrill - to do it for Sheikh Mohammed and Charlie Appleby".
'So we're interrupting, we're peaceful, and I'm telling you the truth about how it's all put together, so your probably need a grinder (to cut the chains)'.
In a statement released by Victoria Racing, the sad news was confirmed. Now in its second year, the world's richest turf race was won for a second straight time by Redzel.
UPDATES: THE horse that exited midway through the Melbourne Cup - the Aidan O'Brien-trained The Cliffsofmoher - has been euthanased.
Jockey Ryan Moore checks on The Cliffsofmoher after it broke down in the first lap of the Melbourne Cup.
The track was downgraded from good to a Heavy 8 before the rain passed, allowing the course to come back to a Soft 6 at race time.