Fraser-Pryce and US sprinter Sha’Carri Richardson, who went on to win silver, were delayed entering the warm-up area after being denied entry by officials at a gate they had previously used.
However, Jamaica chef de mission Ian Kelly later confirmed Fraser-Pryce’s absence was because of injury.
“Mrs Fraser-Pryce was allowed to enter the warm-up track but from another gate from which she was directed to enter from,” he said.
“There is no truth that she was not allowed to enter the stadium. Unfortunately she was not able to compete due to an injury sustained during her final warm-up.”
Fraser-Pryce was bidding to make the 100m podium at a fifth successive Olympics after being denied a third title by team-mate Elaine Thompson-Herah in Tokyo three years ago.
The third-fastest woman in history with a personal best of 10.60 seconds, Fraser-Pryce announced her decision to retire in February – 17 years after she first appeared on the global stage for Jamaica’s 4x100m relay team at the 2007 World Championships.