The race will be her first since the new rules went into effect.
Under the new regulations, female athletes with high natural levels of testosterone wishing to compete in events from 400m to a mile must medically limit that level to under 5 nmol/L, double the normal female range of below 2 nmol/L.
Barring an appeal, Semenya can no longer compete in her specialist event after she lost her appeal against the new rules, with the Court of Arbitration for Sport (CAS) stating that the regulations were necessary to ensure fair competition.
Semenya will form part of a formidable field at the Prefontaine Classic that includes world 5,000-metres champion Hellen Obiri, 2016 world indoor 1,500-metres champion Sifan Hassan, and 2018 world indoor 1,500 and 3,000-metres champion Genzebe Dibaba.
"It was a request from Caster Semenya's agent asking if she could run a 3,000," meet director Tom Jordan told Reuters. "Of course we said yes."
The event is sponsored by Nike, who have Semenya in their stable of athletes.
Semenya became South African national champion in the 5,000 metres in April, but is some way off the leading runners in the world over that distance.
The flat 3,000 metres is not contested at the Olympic Games, but a steeplechase over the distance is on the list of events.
Semenya has a personal best of 9:36.29 in the flat 3,000 metres, the slowest of the runners in the Prefontaine Classic, with Dibaba (8:16.60) the quickest.
The South African’s last race over 800 metres was in the Diamond League in Doha on May 3, when she cruised to victory in 1:54.98, nearly three seconds ahead of Burundi's Francine Niyonsaba.
"I'm a crazy athlete, I switch events like hell but, yeah, 800 metres is my calling, I believe in it, and that's what I want to do," she said after winning in Doha.
"I will switch races when I want to -- no man can tell me what to do. I'm here for a purpose, if I want to switch events I switch them, but if someone wants me to switch them, that's their own problem, not mine.
"I'm a power athlete, I can run from 100 metres to 5 km, so I can run any race I want."
The Prefontaine Classic is being staged in Stanford, California this year while a new stadium is built in Eugene, Oregon for the 2021 world championships.
(Reporting by Nick Said; Additional reporting by Gene Cherry, editing by Pritha Sarkar)
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