Sheikh Mohammed's personal Melbourne Cup drought had stretched three decades back to 1988 when he was first represented in the Cup by Authaal, trained by the late Colin Hayes, which finished 19th.
Sheikh Mohammed bin Rashid Al Maktoum is finally a big victor.
But despite its size and prestige, no Godolphin-bred horse had ever won the Melbourne Cup.
Cross Counter, trained by Charlie Appleby and quoted at 10-1, gets in at a light weight but will be having only its eighth start.
It was the first win for Sheikh Mohammed bin Rashid Al Maktoum's Godolphin, who have been trying to crack the Melbourne Cup since first trying with Faithful Son in 1998.
Charlie Appleby, trainer of Cross Counter, became the first Englishman to ever train a Melbourne Cup victor.
In a statement, RSPCA Australia spokesperson Jane Speechley said: "Our thoughts are with animal lovers across the country who have been affected by this loss, and confronted by the very real risks posed by racing to the horses involved".
A year ago it was reported his efforts to win the Cup, combined with other racing operations Down Under, had set him back $1.1 billion.
"I can't thank everyone enough".
His Cross Counter, a three-year-old bay gelding ridden by Kerrin McEvoy, came from the outside to beat Marmelo by a length to bring home the $2.8 million Melbourne Cup following years of disappointment for the billionaire Dubai ruler.
"It's great to be stood here and it's fantastic for Godolphin", Appleby told CNN affiliate Seven News Australia after Cross Counter and McEvoy's win. It's a day I will never forget.
Aidan O'Brien's head lad TJ Comerford was seen speaking to stewards more than an hour before the Cup, but a Racing Victoria spokesperson said it was only for clarification over what riding tactics the stable might use in the race.
The victory by Cross Counter notched up 30 Group One wins for Godolphin worldwide this year.
There was further drama from the post-race veterinary examination of horses for the two favourites, Magic Circle and Yucatan. "We had plenty of trips away and some good times on the track".
Cross Counter wins the 2018 Melbourne Cup.
Jockey Kerrin McEvoy celebrated his third win in the two-mile race, drawing level with active jockeys Damien Oliver and Glen Boss.
"You get out of bed very early and spend a lot of time on the back of horses. Well done to Charlie and this little horse", McEvoy said.