The Charlie Appleby-trained gelding stormed down the straight from the outside to haul in runner-up and last year's favorite Marmelo by a length, with A Prince of Arran third in the A$7.3 million ($5.26 million) handicap.
It comes four days after he claimed the Breeders' Cup Juvenile Turf in the United States with Line Of Duty.
Earlier in the day the track had been downgraded from good to heavy as heavy rain made life extremely hard for the jockeys and horses in the lead-up races. However, in typical Melbourne fashion, the sun came out and the track condition improved just before the race.
The death of Irish stayer The Cliffsofmoher cast a pall over the Melbourne Cup on Tuesday, angering animal rights groups and shining the spotlight on the safety record of Australia's most prestigious race meeting.
Marmelo and A Prince of Arran ran second and third respectively, as race favourites Yucatan and Magic Circle failed to deliver on pre-race expectations.
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IT was on their many road trips to Yorkshire that aspiring trainer Charlie Appleby and jockey Kerrin McEvoy forged a bond that culminated with Cross Counter becoming the first British victor of the Melbourne Cup. And he has achieved lifted both those most prized of trophies and now won 12 races at the highest level.
"We're only a small team, so to run third in a race like this is remarkable. He had a blank canvas", Appleby said of McEvoy.
In a ideal completion to a stellar year highlighted by Masar's Derby victory, Thunder Snow's Dubai World Cup and 27 other G1s, Cross Counter epitomised the Godolphin philosophy of pushing global boundaries and striving for perfection. "I don't want it to end".
Sheikh Mohammed, the ruler of Dubai, promoted him in 2013 when trainer Mahmood al Zarooni was given an eight-year ban after a doping scandal.
"It's a challenge that's been a long road. It's a very special day and one I will never forget".
Stier said vets were with the horse "all but immediately" and that it had received the best possible care.
Cross Counter's historic victory was described by his British trainer, Charlie Appleby, as "everybody's dream".
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