In roasting mid-afternoon temperatures, Semenya finished 13th in the first of two rounds at Hayward Field, Eugene, in 15:46.12, more than 45sec off the 15th and final qualifying place.
“Cooking!” said Semenya post-race. “It was hot, I could not keep up with the pace, I tried to stick as much as I can, but you know, it is a part of the game.
“I think it is great to be able to run here,” she added. “Just being able to finish the 5k, for me it is a blessing. I am learning and I am willing to learn even more.”
Her time was far off the heat-winning 14:52.64 set by Ethiopian Gudaf Tsegay, fresh from her silver in the 1500m.
Semenya sat 13th of the 18-strong field as Japan’s Kaede Hagitani set the early pace in her heat.
When a nine-strong pack broke clear, it was clear Semenya would not be part of the breakaway and she quickly fell to a full 80 metres off the lead with 2km to go.
That has increased to a clear 100 metres as American Karissa Schweizer hit the lead with three laps to run.
Tsegay kicked and led a pack of five through the bell with Semenya a distant figure 300 metre off the pace.
The South African last competed at a world championships in London in 2017 where she won her third 800m world crown.
A year later she won double gold in the 800m and 1500m at the Commonwealth Games which is the last time she represented South Africa in a global international competition.
Semenya was forced to switch from her favoured distance to the longer event due to gender eligibility rules that required her to take testosterone-reducing drugs to compete in races between 400m to a mile.