Top Queensland galloper Alligator Blood was disqualified and his trainer David Vandyke received a $20,000 fine after a prohibited substance was detected following the gelding's win in the $2 million Magic Millions Guineas on the Gold Coast.

A Racing Queensland stewards inquiry delivered their judgment late on Thursday after a marathon hearing.

Initial runner-up Eleven Eleven has been promoted to first while Exhilarates improves to second and Hightail joins the minor placings.

Alligator Blood's connections have forfeited the $1.1 million winners' cheque after a post-race swab on January 11 revealed traces of altrenogest.

More commonly known as Regu-mate, altrenogest is banned for use on male horses.

It is a hormone given to keep female horses from being in season, or if they are already pregnant, to keep them from losing the foal.

Vandyke avoided suspension after being found guilty of breaching rule AR240(2).

He was charged with presenting a horse to race with a prohibited substance, not the more serious administrating charge.

Alligator Blood's owner Allan Endresz confirmed he will challenge the decision in the Supreme Court.

"From the trainer's perspective, collectively we are very happy," Endresz told racing.com

"But what did come out of it was they have stuck the mandatory rule 240 that the horse is automatically disqualified. That's consistent with what I've been saying, that there was no wriggle room.

"That will be the undoing when I start to hit my straps. I have been talking about it (heading to the Supreme Court) for a long time," he said.

"We will debrief our legal views to QRIC so we are up front about that."

Alligator Blood's penalty is Queensland racing's highest profile disqualification since Ducatoon was stripped off the 1980 Stradbroke Handicap after the mare returned a positive swab.

Media were barred from attending the proceedings by stewards, so details were limited to a short statement released by the Queensland Racing Integrity Commission.

Alligator Blood has won two races since the Magic Millions Guineas, including the Group One Australian Guineas at Flemington and all swabs were clear.