The council also voted to tighten restrictions on athletes with Differences in Sex Development (DSD), cutting the maximum amount of plasma testosterone for athletes in half, to 2.5 nanomoles per litre from five.
World Athletics president Sebastian Coe told a news conference that the decision to exclude transgender women was based "on the overarching need to protect the female category".
The governing body had previously floated the option of transgender athletes being allowed to compete in the female category if they, too, maintained testosterone levels below 2.5 nanomoles per litre for 24 months.
Yet it said on Thursday that it became apparent there was little support within the sport for that proposal.
"We're not saying no forever," Coe said, adding that WA would form a task force to study the issue of trans inclusion that would be chaired by a transgender athlete.
DSD athletes will have to reduce their testosterone levels below the new limit for a minimum of 24 months to compete internationally in any elite event in the female category, WA said in a statement.
The tighter rules will impact DSD athletes such as two-times Olympic 800 metre champion Caster Semenya, Christine Mboma, the 2020 Olympic silver medallist in the 200m, and Francine Niyonsaba, who finished runner-up to Semenya in the 800 at the 2016 Olympics.
WA regulations around DSD previously required women competing in events between 400 metres and a mile to maintain testosterone levels below five nanomoles per litre.
At the 2020 Olympics, South Africa's Semenya and Burundi's Niyonsaba were both barred from the 800m before turning their attention to the 5,000.
Semenya failed to qualify for the Games while Niyonsaba made the final before being disqualified for a lane violation.
Namibia's Mboma, prevented from running the 400m, switched to the 200m, winning silver.
DSD athletes have male testes but do not produce enough of the hormone Dihydrotestosterone (DHT) that is necessary for the formation of male external genitalia.
Swimming's world governing body World Aquatics voted last June to bar transgender women from elite competition if they had experienced any part of male puberty. A scientific panel had found that even after reducing their testosterone levels through medication, transgender women still had a significant advantage.
The vote passed with 71% of the national federations in favour.
