Jeremy Noseda’s four-year-old had been one of the leading contenders for the Flemington showpiece after landing the Irish St Leger at the Curragh.
He had been in quarantine for almost a fortnight but will now not travel to Australia.
Barry Simpson, racing manager for owner Sir Robert Ogden, said: “He suffered a severe attack of azoturia (muscle stiffness) after he finished work on the (Newmarket) Heath on Tuesday night.
“It’s hugely disappointing for Sir Robert and everyone involved.
“We were all looking forward to having a runner in such a famous and prestigious race.”
Meanwhile, Criquette Head-Maarek believes Helleborine could become her fifth 1000 Guineas winner next May following her fine effort in defeat at Longchamp on Sunday.
The two-year-old was defending an unbeaten record in the Prix Marcel Boussac but after travelling ominously well for much of the contest, she could not pass Aidan O’Brien’s tough filly Misty For Me.
Head-Maarek, who has trained Ma Biche (1983), Ravinella (1988), Hatoof (1992) and this year Special Duty (2010) to take Classic glory at Newmarket, is far from despondent however, and believes there is still plenty to look forward to.
“She looks very well and she ran a very good race,” said the French trainer.
“She came very fast, very quickly and maybe came a little bit too soon going too fast. She’s got a tremendous turn of foot, but the winner must be a very good filly also.
“I thought our filly was going to make it but the winner went again – it was nothing to be ashamed of.
“She won’t run again this year but we will enter her in the 1000 Guineas at Newmarket.
“We will also put her in the French Guineas and then decide where we are going to go, but the English Guineas is a race I like and she is the kind of filly for that race if I can have her in good form.
“If we go for the Guineas she will have a prep race in the Prix Imprudence at Maisons-Laffitte in April.