Great Britain have had no shortage of track misery at the 2020 Games and the 27-year-old was the latest victim.
Gemili had his right thigh heavily strapped up but pulled up immediately in the Olympic Stadium in Tokyo.
He revealed afterwards that he had torn his hamstring in his last blocks session before final call, finishing the distance in 1 minute 58.58 seconds after an emotional trudge to the line.
"The last run, literally the last run before I came into the call room, the last blocks start and I felt it go," he said.
"It's my hamstring. I had to try but I'm in so much pain right now. I said to my physio, ‘just strap it up and let me at least try to push out’ but I can tell straight away.
"You don't just cramp up when you sprint, it was a tear. I can't believe this has happened."
Gemili narrowly finished fourth in the final in Rio five years ago and also came fourth at the 2019 World Championships.
Team GB have won just one medal in the Olympic Stadium, with Keely Hodgkinson taking silver in the women's 800m, after Zharnel Hughes false-started in the 100m final and Reece Prescod was also disqualified in the semi-finals.
Dina Asher-Smith suffered a serious hamstring injury last month and pulled out of the 200m after failing to reach the 100m final while Katarina Johnson-Thompson comes into the heptathlon on Wednesday after rupturing her Achilles in December.
Nethaneel Mitchell-Blake also failed to qualify after coming fifth in his heat in 20.56secs.
Jake Wightman at least reached the 1500m semi-finals after coming through his heat unscathed, the 27-year-old finishing third in 3 minutes 41.18secs at the Olympic Stadium on Tuesday.
Team-mate Josh Kerr finished seventh in his heat, running a time of 3 minutes 36.29secs, with only the top six qualifying automatically, but will progress as one of the next six fastest.
Jake Heywood won his heat to also go through and Jodie Williams and Ama Pipi reached the 400m semi-finals, with Nicole Yeargin disqualified for a lane infringement.