Instead of running in the Champagne Stakes at Randwick, Intrusion will end his first racing campaign in a restricted race at Warwick Farm.
Trainer Gerald Ryan had hoped the colt could make it as far as Saturday's Group One race for two-year-olds but it wasn't to be.
He hopes Intrusion can go out on a high on Wednesday and takes confidence from his last-start third at Rosehill on April 1.
The 1200m race was won by Sempre Libera who was an unlucky runner in Saturday's Group Three Percy Sykes Stakes, finishing fourth in a tight finish, less than half a length from the winner.
"He is a well-bred horse I thought would be an ideal Champagne Stakes type," Ryan said.
"But he just wasn't quite ready.
"It was a good race he was in last time and the form says that.
"He will go to the paddock after Warwick Farm and come back for the spring."
A $600,000 yearling by Redoute's Choice out of unraced American mare Fleeting Touch, Intrusion goes to Wednesday's race for his third start after beginning his career with an unplaced run in the Group Two Pago Pago Stakes.
After the race he will be joined in the spelling paddock by stablemate Perignon who missed the Group One Sires' Produce Stakes with a temperature and was then ruled out of the Percy Sykes with a leg injury.
There were fears she had injured a tendon but a relieved Ryan said things were not as bad as they first seemed.
"We had the leg scanned and everything is good," Ryan said.
"It appears she has twisted a fetlock joint and the swelling has run up the tendon but the tendon itself is fine.
"We'll give her a rest and get her ready for spring."
The Snitzel filly has had five starts for a 1200m win at Canterbury and a close second in the Group Two Magic Night Stakes.