For the first time in the event's 40 year history, the 160km race was called off 60km short of the finish, with just two legs remaining.
Torrential rain dogged the event from the midnight start, with riders reporting atrocious conditions and horses slipping and falling.
When the race was called off at 10.30am at the end of the third leg, almost one- third of 130 horses competing had been vetted out or withdrawn by their owners because of the conditions.
A US rider reportedly fell in the early stage of the race and suffered broken nose cartilage.
The four leading riders had already set off on the fourth and second last leg of the endurance event when organisers made the decision to end the race.
Event committee chairman Geoff Becker said the course had become too dangerous for horses and riders.
"We can't get our rescue vehicles in if someone gets hurt and we were not prepared to take the risk," he said.
"The decision caused us a great deal of angst but we wanted to do the right thing for the sport."
Mr Becker said he did not believe the decision tarnished the spirit of the Tom Quilty.
"The ride was still conducted in the spirit of an endurance ride," he said.
There is no provision in the rules for awarding places in such a situation.
After consulting members of the Australian Endurance Riders Association, the committee agreed the Tom Quilty Gold Cup would be presented to the leading place-getters at the end of the third leg, pending fitness of horses.
The cup was awarded jointly to Peter and Jenny Toft and Abdullah Kharis Ali Saeed of the Toft Endurance team from near Brisbane.
Brooke Warner, 14, of the Toft team was the first junior to finish.
Mr Toft rode nine-year old appaloosa Murdoch, a Tasmanian-bred horse ranked number one in Australia.
"The track was very slippery and deteriorating as we rode," he said.
"It was potentially very dangerous for the riders. I congratulate the committee on a brave decision which has not been done before in all these years. We're disappointed, we were prepared to challenge for it, win or lose on the conditions of the day. We would have like to take home the gold cup under different circumstances. It is probably not the first time it should have been stopped - like in 1998. So the decision today is exactly the ethos of the event. The horses and riders always come before the competition."
Victorian veterinarian Brian Sheahan said the conditions were not a threat to the horses but fallen riders could very quickly suffer hypothermia and help would not be able to reach them. Mr Saeed, from the United Arab Emirates, and a member of the Toft team, became the first international rider to win the event.
"It was the first time in my life I've been in so rough conditions. If you finish 100km in this weather, you're a winner," he said.
Riders reported mixed feelings about the decision: disappointment tinged with relief. Three-time Quilty winner and champion Australian rider Meg Wade, from Victoria, said the conditions were the worst she had seen in the race. At the end of the first leg she was so wet she had to totally change her clothes, even wringing out her underpants and socks.
She said that early in the race there were places where horses could get no footing at all in the slippery conditions and there were deep puddles. Headlamps were rendered useless in the fog.
"The horses weren't enjoying it even though they were coming through their vet checks well. There were a number of falls on the track," she said. "The reason they're (the horses) here is because of us, and if we want to do it we need to think of them and get over the ego of competing."
Ms Wade said there were some positives to come out of the disaster. "Because they've been brave enough to make this decision - and I've been at others that probably should have been cancelled - now people will say it can be done."
Chief steward Linda Tanian, of Victoria, said the decision was disappointing for both competitors and organisers, who had spent two years preparing the event. "It was a gutsy decision," she said.
Drama began for the 2005 Tom Quilty even before the start. Miss Warner felt dizzy and fainted on Friday and was taken to the Mersey General Hospital at Latrobe.
"They said I shouldn't ride but I said I thought I was well enough," Miss Warner said. She has already ridden the 160km distance three times and competed in the Tom Quilty in 2003.
Despite the conditions, the decision to curtail the race was not without controversy.
Patron of the 2005 event and veteran of 21 Tom Quilty rides Ron Males supported the decision to cut the race short. "Once it becomes dangerous, you have to stop. You can't replace people," he said. "Once you fail on safety you wouldn't be able to get insurance cover."
However, Mr Males said he also supported the decision by some riders not to accept the Tom Quilty silver buckle awarded to all riders who finish the race.
"They don't believe they've done the distance," he said.
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