Trainer Lee Freedman made the decision on Wednesday morning after not being 100% satisfied with the gelding's condition.
"Mr Malek won't be running in the Guineas. I'm just not happy with him going into that race," said the Australian.
A winner of six from eight starts, the son of Swiss Ace was widely regarded as likely favourite Inferno's main danger in the third and last Leg of the Singapore Three-Year-Old Challenge.
With Mr Malek's non-participation, the number of entries is now down to nine. The withdrawal of such a leading hope might take the gloss out of Saturday's feature, but the likes of Rocket Star and Strong N Powerful are still regarded as potential threats to Inferno's supremacy.
Mr Malek was to be partnered by A'Isisuhairi Kasim, who just the day before, was oozing a certain quiet confidence ahead of the race.