The Melbourne Cup witnessed a fourth death since 2013 as The Cliffsofmoher was euthanised on the track.
Meanwhile, second and third place went to Marmelo and A Prince Of Arran.
"Once he found those and the horse had a clear run, I was far from confident but I knew he would be doing his best work down the straight".
"Charlie was travelling head lad when I was with Godolphin in the United Kingdom and we used to head up to all the Northern tracks a lot of the time".
"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", Jamie Stier, Racing Victoria's manager of integrity services, said.
Jockey Kerrin McEvoy celebrated his third win in the grueling two-mile race, drawing level with active jockeys Damien Oliver and Glen Boss.
It was also a first win in the race for Sheikh Mohammed's Godolphin team, for whom Appleby saddled Masar to their maiden Derby win at Epsom in June.
McEvoy's win on the 9-1 shot followed his Melbourne Cup triumphs on Almandin in 2016 and Brew in 2000. I'm just in a fortunate position to have the horses to make the call on which are the right ones to bring down here.More news: Li Haotong overtakes Justin Rose as Shubhankar stays 53rd in Turkey
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Yucatan started favourite in the race at 5-1 after drifting to 7-1 following the barrier draw that saw him jump from gate 23.
The victory had strong a connection to Sheikh Mohammed's Darley stallion operation through his sire Teofilo for whom he became a 15th G1 victor. "This year has just been one of those wonderful years".
Appleby admitted on Tuesday that winning the race for the Dubai outfit ticked off a box on his bucket list, but while the English trainer was able to bask in the glory of victory, he was later also quick to praise his boss and the team.
"I did promise (the kids) a swimming pool".
McEvoy, like Appleby, was quick to praise Sheikh Mohammed.
Cross Counter and Kerrin McEvoy win the Melbourne Cup.
After some fallow years, this season has proved to be stellar one for Godolphin, which ended the British Flat racing season as the leading owner, claiming 113 wins, including its first Epsom Derby, and winning 4.5 million in prize money, according to the website of the British Horseracing Authority.
That's because of increasing attention being given to The Everest in mid-October.