The 24-year-old has been battling an adductor problem and will now not run on Monday night at the Gold Coast’s Carrara Stadium.
He had qualified for the final third fastest and told Press Association Sport after Sunday’s semi final he was hopeful of racing.
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Gemili has also been ruled out of the 4x100m relay on Saturday.
“I’m hugely gutted to announce that I have had to withdraw from the 100m final due to an injury sustained in the semi final,” he confirmed on Twitter.
“I am so proud to represent Team England and it’s devastating not to have the chance to compete tonight but the doctors have said I am unable to take part.
“I want to thank everyone for their kind messages of support and love. I’m looking forward to cheering on the rest of the team and getting back to competing shortly!”
2018 Commonwealth Games – Day Four
Image credit: PA Sport
Gemili, who helped GB win the 4x100m relay at last year’s World Championships, ran 10.11 seconds in the semi-final to qualify behind Jamaica’s Yohan Blake and Kemar Hyman of the Cayman Islands.
But he was clearly in discomfort immediately afterwards, although he remained hopeful of making Monday’s final.
He said on Sunday: “I had a bit of an adductor injury a few day ago and I did feel it a little in the semi-final. I’ll go and see the physio and rest up and get it ready.
“No, it won’t bother me. It’s 100m, I’ll put my body there and run as best as I can. I leave everything on the track.
“The start wasn’t as good as I’d like it to be, I left myself a lot of work. Yohan is a former world champion so everyone is pinning him as the favourite but anything can happen. One mistake in the 100m and it’s game over.”
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