The 30-year-old won the title in 15 minutes 52.28 seconds - 42.48 seconds outside the Olympic qualifying time.
"I'm getting old‚ I'm scared to tear my muscles," she said of the 200m event.
The qualifying deadline for Tokyo is 29 June.
Semenya is a two-time Olympic champion in the 800m and won the 1,500m at the Commonwealth Games in 2018.
https://www.youtube.com/watch?v=psxr58zKi6gBut under World Athletics rules, she is not allowed to compete in events between 400m and a mile unless she takes drugs to reduce her naturally high levels of testosterone.
She said in March 2019 that she would aim to compete in the 200m in Tokyo, but now feels it would be too much pressure on her body.
"We had to sit down and make sure that the decision that we make makes sense. Distance makes sense.
"We're happy with what we're doing‚ we're having fun. At training each and every day, we don't stress."